Starting phenix.real_space_refine on Fri Feb 23 10:13:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9b_4479/02_2024/6q9b_4479_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9b_4479/02_2024/6q9b_4479.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9b_4479/02_2024/6q9b_4479_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9b_4479/02_2024/6q9b_4479_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9b_4479/02_2024/6q9b_4479_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9b_4479/02_2024/6q9b_4479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9b_4479/02_2024/6q9b_4479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9b_4479/02_2024/6q9b_4479_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9b_4479/02_2024/6q9b_4479_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 276 5.16 5 C 24847 2.51 5 N 6172 2.21 5 O 6700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D1 ARG 62": "NH1" <-> "NH2" Residue "D1 TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 195": "NH1" <-> "NH2" Residue "D1 TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 ARG 173": "NH1" <-> "NH2" Residue "D5 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D4 TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ARG 19": "NH1" <-> "NH2" Residue "B5 ARG 26": "NH1" <-> "NH2" Residue "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 305": "NH1" <-> "NH2" Residue "A3 ARG 46": "NH1" <-> "NH2" Residue "B3 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ARG 5": "NH1" <-> "NH2" Residue "C2 ARG 120": "NH1" <-> "NH2" Residue "B4 ARG 41": "NH1" <-> "NH2" Residue "AM ARG 81": "NH1" <-> "NH2" Residue "B9 ARG 92": "NH1" <-> "NH2" Residue "B9 ARG 128": "NH1" <-> "NH2" Residue "B9 ARG 176": "NH1" <-> "NH2" Residue "B8 ARG 70": "NH1" <-> "NH2" Residue "A1 ARG 25": "NH1" <-> "NH2" Residue "A1 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38012 Number of models: 1 Model: "" Number of chains: 37 Chain: "S2" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 325 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 7, 'TRANS': 31} Chain: "D3" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 728 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "D1" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2400 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 278} Chain breaks: 1 Chain: "D6" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1308 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 164} Chain breaks: 1 Chain: "4L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "D5" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4805 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Chain: "D4" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3646 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Chain: "D2" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2724 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain: "AK" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1025 Classifications: {'peptide': 140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "B5" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1156 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "AB" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A8" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 156} Chain: "BJ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "AJ" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2583 Classifications: {'peptide': 319} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain: "S5" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "A3" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 62} Chain: "B3" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C2" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 997 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 107} Chain: "B4" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 117} Chain: "AM" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 945 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B6" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 804 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 12, 'TRANS': 82} Chain breaks: 1 Chain: "B7" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1026 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "B9" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1515 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 16, 'TRANS': 159} Chain: "B2" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "B8" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1324 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 135} Chain: "BK" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 853 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 93} Chain: "C1" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 391 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "B1" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 449 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "A1" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "D6" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "D5" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 200 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 102 Chain: "D4" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 71 Chain: "AK" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "B5" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "AB" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "A8" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "B4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 26 Time building chain proxies: 21.38, per 1000 atoms: 0.56 Number of scatterers: 38012 At special positions: 0 Unit cell: (221.2, 134.4, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 276 16.00 P 17 15.00 O 6700 8.00 N 6172 7.00 C 24847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSAK 17 " - pdb=" SG CYSAK 74 " distance=2.03 Simple disulfide: pdb=" SG CYSAK 94 " - pdb=" SG CYSAK 114 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 35 " - pdb=" SG CYSA8 65 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 45 " - pdb=" SG CYSA8 55 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 77 " - pdb=" SG CYSA8 109 " distance=2.02 Simple disulfide: pdb=" SG CYSA8 87 " - pdb=" SG CYSA8 99 " distance=2.03 Simple disulfide: pdb=" SG CYSBJ 76 " - pdb=" SG CYSBJ 83 " distance=2.04 Simple disulfide: pdb=" SG CYSBJ 112 " - pdb=" SG CYSBJ 124 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 32 " - pdb=" SG CYSS5 65 " distance=2.04 Simple disulfide: pdb=" SG CYSS5 42 " - pdb=" SG CYSS5 55 " distance=2.04 Simple disulfide: pdb=" SG CYSB7 58 " - pdb=" SG CYSB7 89 " distance=2.03 Simple disulfide: pdb=" SG CYSB7 68 " - pdb=" SG CYSB7 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.36 Conformation dependent library (CDL) restraints added in 7.0 seconds 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8772 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 2 sheets defined 57.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.07 Creating SS restraints... Processing helix chain 'S2' and resid 8 through 12 Processing helix chain 'D3' and resid 2 through 23 Processing helix chain 'D3' and resid 53 through 78 removed outlier: 4.238A pdb=" N VALD3 58 " --> pdb=" O LYSD3 54 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALAD3 59 " --> pdb=" O PHED3 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILED3 60 " --> pdb=" O PHED3 56 " (cutoff:3.500A) Proline residue: D3 74 - end of helix removed outlier: 5.370A pdb=" N TRPD3 77 " --> pdb=" O LEUD3 73 " (cutoff:3.500A) Processing helix chain 'D3' and resid 84 through 107 Processing helix chain 'D1' and resid 2 through 31 Proline residue: D1 12 - end of helix removed outlier: 3.931A pdb=" N LEUD1 15 " --> pdb=" O ILED1 11 " (cutoff:3.500A) Processing helix chain 'D1' and resid 46 through 57 Processing helix chain 'D1' and resid 68 through 84 Proline residue: D1 75 - end of helix Processing helix chain 'D1' and resid 102 through 123 Processing helix chain 'D1' and resid 127 through 154 removed outlier: 4.803A pdb=" N TYRD1 142 " --> pdb=" O GLND1 138 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLUD1 143 " --> pdb=" O THRD1 139 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VALD1 144 " --> pdb=" O ILED1 140 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THRD1 145 " --> pdb=" O SERD1 141 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALAD1 147 " --> pdb=" O GLUD1 143 " (cutoff:3.500A) Processing helix chain 'D1' and resid 163 through 168 Processing helix chain 'D1' and resid 179 through 192 Processing helix chain 'D1' and resid 220 through 241 Processing helix chain 'D1' and resid 252 through 274 Processing helix chain 'D1' and resid 282 through 311 Proline residue: D1 295 - end of helix Proline residue: D1 308 - end of helix Processing helix chain 'D6' and resid 5 through 21 Processing helix chain 'D6' and resid 26 through 47 Processing helix chain 'D6' and resid 51 through 59 removed outlier: 3.576A pdb=" N PHED6 57 " --> pdb=" O GLYD6 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILED6 59 " --> pdb=" O METD6 55 " (cutoff:3.500A) Processing helix chain 'D6' and resid 65 through 75 removed outlier: 3.619A pdb=" N ALAD6 75 " --> pdb=" O THRD6 71 " (cutoff:3.500A) Processing helix chain 'D6' and resid 87 through 108 Processing helix chain 'D6' and resid 138 through 143 Processing helix chain 'D6' and resid 151 through 171 removed outlier: 3.729A pdb=" N ILED6 155 " --> pdb=" O THRD6 151 " (cutoff:3.500A) Processing helix chain '4L' and resid 3 through 20 Processing helix chain '4L' and resid 27 through 50 Processing helix chain '4L' and resid 58 through 83 Processing helix chain 'D5' and resid 2 through 13 Processing helix chain 'D5' and resid 17 through 23 Processing helix chain 'D5' and resid 32 through 57 removed outlier: 4.732A pdb=" N ILED5 49 " --> pdb=" O ILED5 45 " (cutoff:3.500A) Proline residue: D5 50 - end of helix Processing helix chain 'D5' and resid 84 through 88 Processing helix chain 'D5' and resid 90 through 106 Processing helix chain 'D5' and resid 114 through 133 Processing helix chain 'D5' and resid 137 through 155 Processing helix chain 'D5' and resid 162 through 193 Processing helix chain 'D5' and resid 198 through 203 Processing helix chain 'D5' and resid 210 through 223 Processing helix chain 'D5' and resid 232 through 238 Processing helix chain 'D5' and resid 241 through 249 Processing helix chain 'D5' and resid 257 through 262 Processing helix chain 'D5' and resid 271 through 292 Processing helix chain 'D5' and resid 298 through 318 Processing helix chain 'D5' and resid 322 through 349 Processing helix chain 'D5' and resid 368 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 4.328A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYSD5 392 " --> pdb=" O GLYD5 388 " (cutoff:3.500A) Processing helix chain 'D5' and resid 408 through 431 Processing helix chain 'D5' and resid 448 through 470 removed outlier: 5.615A pdb=" N GLYD5 465 " --> pdb=" O SERD5 461 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHED5 466 " --> pdb=" O LEUD5 462 " (cutoff:3.500A) Processing helix chain 'D5' and resid 489 through 508 Processing helix chain 'D5' and resid 519 through 524 Processing helix chain 'D5' and resid 528 through 546 Proline residue: D5 538 - end of helix removed outlier: 3.673A pdb=" N LEUD5 542 " --> pdb=" O PROD5 538 " (cutoff:3.500A) Processing helix chain 'D5' and resid 555 through 561 Processing helix chain 'D5' and resid 563 through 577 Processing helix chain 'D5' and resid 584 through 599 Processing helix chain 'D4' and resid 2 through 16 Proline residue: D4 7 - end of helix removed outlier: 3.820A pdb=" N METD4 12 " --> pdb=" O THRD4 8 " (cutoff:3.500A) Proline residue: D4 13 - end of helix removed outlier: 3.652A pdb=" N TRPD4 16 " --> pdb=" O METD4 12 " (cutoff:3.500A) Processing helix chain 'D4' and resid 23 through 41 removed outlier: 3.930A pdb=" N LEUD4 41 " --> pdb=" O THRD4 37 " (cutoff:3.500A) Processing helix chain 'D4' and resid 60 through 79 Proline residue: D4 64 - end of helix Proline residue: D4 74 - end of helix Processing helix chain 'D4' and resid 89 through 110 Processing helix chain 'D4' and resid 115 through 135 Proline residue: D4 128 - end of helix removed outlier: 4.036A pdb=" N ILED4 131 " --> pdb=" O VALD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 142 through 157 Processing helix chain 'D4' and resid 159 through 170 Processing helix chain 'D4' and resid 176 through 179 No H-bonds generated for 'chain 'D4' and resid 176 through 179' Processing helix chain 'D4' and resid 191 through 206 Processing helix chain 'D4' and resid 210 through 212 No H-bonds generated for 'chain 'D4' and resid 210 through 212' Processing helix chain 'D4' and resid 214 through 221 removed outlier: 4.535A pdb=" N LYSD4 218 " --> pdb=" O LEUD4 214 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALAD4 219 " --> pdb=" O TRPD4 215 " (cutoff:3.500A) Processing helix chain 'D4' and resid 225 through 248 removed outlier: 4.602A pdb=" N LEUD4 248 " --> pdb=" O METD4 244 " (cutoff:3.500A) Processing helix chain 'D4' and resid 253 through 257 Processing helix chain 'D4' and resid 259 through 277 removed outlier: 3.993A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 302 removed outlier: 4.257A pdb=" N ILED4 286 " --> pdb=" O LEUD4 282 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALAD4 287 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 336 Processing helix chain 'D4' and resid 355 through 366 Processing helix chain 'D4' and resid 373 through 388 Processing helix chain 'D4' and resid 393 through 414 removed outlier: 3.908A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 449 Proline residue: D4 443 - end of helix Processing helix chain 'D2' and resid 3 through 22 Processing helix chain 'D2' and resid 26 through 41 Processing helix chain 'D2' and resid 50 through 79 Processing helix chain 'D2' and resid 92 through 106 Processing helix chain 'D2' and resid 112 through 120 Proline residue: D2 116 - end of helix Processing helix chain 'D2' and resid 124 through 148 Proline residue: D2 138 - end of helix removed outlier: 3.897A pdb=" N VALD2 141 " --> pdb=" O ALAD2 137 " (cutoff:3.500A) Proline residue: D2 147 - end of helix Processing helix chain 'D2' and resid 151 through 167 Processing helix chain 'D2' and resid 175 through 193 removed outlier: 4.345A pdb=" N VALD2 193 " --> pdb=" O TRPD2 189 " (cutoff:3.500A) Processing helix chain 'D2' and resid 198 through 220 Processing helix chain 'D2' and resid 227 through 236 Processing helix chain 'D2' and resid 239 through 252 Processing helix chain 'D2' and resid 261 through 271 removed outlier: 3.595A pdb=" N METD2 265 " --> pdb=" O METD2 261 " (cutoff:3.500A) Processing helix chain 'D2' and resid 277 through 300 removed outlier: 4.065A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYRD2 293 " --> pdb=" O ASND2 289 " (cutoff:3.500A) Processing helix chain 'D2' and resid 311 through 316 removed outlier: 4.730A pdb=" N GLND2 316 " --> pdb=" O LYSD2 312 " (cutoff:3.500A) Processing helix chain 'D2' and resid 327 through 334 Processing helix chain 'D2' and resid 340 through 345 removed outlier: 3.973A pdb=" N SERD2 344 " --> pdb=" O PROD2 341 " (cutoff:3.500A) Processing helix chain 'AK' and resid 2 through 10 Processing helix chain 'AK' and resid 19 through 41 Processing helix chain 'AK' and resid 48 through 80 Processing helix chain 'AK' and resid 87 through 104 Processing helix chain 'AK' and resid 107 through 130 Processing helix chain 'B5' and resid 15 through 30 Processing helix chain 'B5' and resid 34 through 46 Processing helix chain 'B5' and resid 70 through 78 Processing helix chain 'B5' and resid 83 through 117 Processing helix chain 'B5' and resid 130 through 132 No H-bonds generated for 'chain 'B5' and resid 130 through 132' Processing helix chain 'AB' and resid 8 through 20 Processing helix chain 'AB' and resid 44 through 58 Processing helix chain 'AB' and resid 64 through 67 No H-bonds generated for 'chain 'AB' and resid 64 through 67' Processing helix chain 'AB' and resid 73 through 84 Processing helix chain 'A8' and resid 21 through 26 Processing helix chain 'A8' and resid 28 through 33 Processing helix chain 'A8' and resid 39 through 48 Processing helix chain 'A8' and resid 56 through 75 Processing helix chain 'A8' and resid 80 through 89 Processing helix chain 'A8' and resid 101 through 113 Processing helix chain 'BJ' and resid 28 through 57 removed outlier: 4.883A pdb=" N ARGBJ 42 " --> pdb=" O LEUBJ 38 " (cutoff:3.500A) Proline residue: BJ 43 - end of helix Processing helix chain 'BJ' and resid 81 through 116 removed outlier: 5.135A pdb=" N GLUBJ 86 " --> pdb=" O LEUBJ 82 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 125 through 141 Processing helix chain 'BJ' and resid 152 through 172 Processing helix chain 'AJ' and resid 5 through 10 Processing helix chain 'AJ' and resid 36 through 45 Processing helix chain 'AJ' and resid 58 through 61 No H-bonds generated for 'chain 'AJ' and resid 58 through 61' Processing helix chain 'AJ' and resid 79 through 84 Processing helix chain 'AJ' and resid 94 through 116 Processing helix chain 'AJ' and resid 128 through 140 Processing helix chain 'AJ' and resid 146 through 162 removed outlier: 4.382A pdb=" N CYSAJ 161 " --> pdb=" O LYSAJ 157 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLUAJ 162 " --> pdb=" O VALAJ 158 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 176 through 186 Processing helix chain 'AJ' and resid 189 through 192 No H-bonds generated for 'chain 'AJ' and resid 189 through 192' Processing helix chain 'AJ' and resid 197 through 208 Processing helix chain 'AJ' and resid 210 through 214 Processing helix chain 'AJ' and resid 231 through 239 Processing helix chain 'AJ' and resid 247 through 249 No H-bonds generated for 'chain 'AJ' and resid 247 through 249' Processing helix chain 'AJ' and resid 254 through 263 Processing helix chain 'AJ' and resid 270 through 272 No H-bonds generated for 'chain 'AJ' and resid 270 through 272' Processing helix chain 'AJ' and resid 286 through 297 Processing helix chain 'S5' and resid 5 through 8 No H-bonds generated for 'chain 'S5' and resid 5 through 8' Processing helix chain 'S5' and resid 33 through 42 Processing helix chain 'S5' and resid 50 through 54 Processing helix chain 'S5' and resid 56 through 66 Processing helix chain 'S5' and resid 69 through 88 Processing helix chain 'A3' and resid 16 through 30 Processing helix chain 'A3' and resid 38 through 46 Processing helix chain 'B3' and resid 26 through 38 Processing helix chain 'B3' and resid 62 through 66 Processing helix chain 'B3' and resid 69 through 71 No H-bonds generated for 'chain 'B3' and resid 69 through 71' Processing helix chain 'B3' and resid 73 through 82 Processing helix chain 'C2' and resid 16 through 19 Processing helix chain 'C2' and resid 29 through 48 Processing helix chain 'C2' and resid 58 through 96 Processing helix chain 'B4' and resid 26 through 48 Processing helix chain 'B4' and resid 62 through 71 Processing helix chain 'B4' and resid 83 through 117 removed outlier: 3.564A pdb=" N ILEB4 94 " --> pdb=" O ALAB4 90 " (cutoff:3.500A) Proline residue: B4 96 - end of helix Processing helix chain 'AM' and resid 31 through 96 Proline residue: AM 72 - end of helix Processing helix chain 'AM' and resid 130 through 135 Processing helix chain 'B6' and resid 5 through 24 Processing helix chain 'B6' and resid 68 through 91 Proline residue: B6 77 - end of helix removed outlier: 3.680A pdb=" N TYRB6 87 " --> pdb=" O TYRB6 83 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HISB6 88 " --> pdb=" O TYRB6 84 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VALB6 89 " --> pdb=" O LEUB6 85 " (cutoff:3.500A) Processing helix chain 'B7' and resid 3 through 9 Processing helix chain 'B7' and resid 42 through 47 Processing helix chain 'B7' and resid 60 through 71 Processing helix chain 'B7' and resid 81 through 118 Processing helix chain 'B9' and resid 11 through 29 Processing helix chain 'B9' and resid 34 through 49 Processing helix chain 'B9' and resid 57 through 71 Processing helix chain 'B9' and resid 92 through 96 removed outlier: 4.099A pdb=" N CYSB9 95 " --> pdb=" O ARGB9 92 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYRB9 96 " --> pdb=" O TYRB9 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B9' and resid 92 through 96' Processing helix chain 'B9' and resid 108 through 113 Processing helix chain 'B9' and resid 115 through 130 Processing helix chain 'B9' and resid 134 through 140 Processing helix chain 'B9' and resid 167 through 170 No H-bonds generated for 'chain 'B9' and resid 167 through 170' Processing helix chain 'B2' and resid 19 through 40 Processing helix chain 'B8' and resid 5 through 7 No H-bonds generated for 'chain 'B8' and resid 5 through 7' Processing helix chain 'B8' and resid 18 through 26 Processing helix chain 'B8' and resid 81 through 83 No H-bonds generated for 'chain 'B8' and resid 81 through 83' Processing helix chain 'B8' and resid 99 through 121 Processing helix chain 'BK' and resid 51 through 63 removed outlier: 3.780A pdb=" N VALBK 55 " --> pdb=" O PROBK 51 " (cutoff:3.500A) Processing helix chain 'BK' and resid 70 through 78 Processing helix chain 'BK' and resid 87 through 102 Processing helix chain 'BK' and resid 115 through 117 No H-bonds generated for 'chain 'BK' and resid 115 through 117' Processing helix chain 'C1' and resid 16 through 45 Processing helix chain 'B1' and resid 15 through 33 Processing helix chain 'A1' and resid 6 through 15 Processing helix chain 'A1' and resid 18 through 29 Processing helix chain 'A1' and resid 42 through 53 Processing sheet with id= A, first strand: chain 'D5' and resid 61 through 67 Processing sheet with id= B, first strand: chain 'AJ' and resid 122 through 125 removed outlier: 6.834A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) 1893 hydrogen bonds defined for protein. 5613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.63 Time building geometry restraints manager: 16.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6994 1.33 - 1.45: 10460 1.45 - 1.58: 21036 1.58 - 1.71: 35 1.71 - 1.84: 499 Bond restraints: 39024 Sorted by residual: bond pdb=" C13 ZMPAB 101 " pdb=" N1 ZMPAB 101 " ideal model delta sigma weight residual 1.487 1.341 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" C16 ZMPAB 101 " pdb=" N2 ZMPAB 101 " ideal model delta sigma weight residual 1.474 1.334 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C PROS5 94 " pdb=" N PROS5 95 " ideal model delta sigma weight residual 1.336 1.408 -0.072 1.08e-02 8.57e+03 4.46e+01 bond pdb=" C10 ZMPAB 101 " pdb=" S1 ZMPAB 101 " ideal model delta sigma weight residual 1.852 1.723 0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" OB3 CDLAK 501 " pdb=" PB2 CDLAK 501 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.00e-02 1.00e+04 2.60e+01 ... (remaining 39019 not shown) Histogram of bond angle deviations from ideal: 95.35 - 104.24: 900 104.24 - 113.13: 21051 113.13 - 122.02: 24093 122.02 - 130.91: 6557 130.91 - 139.81: 293 Bond angle restraints: 52894 Sorted by residual: angle pdb=" C CYSAK 17 " pdb=" N HISAK 18 " pdb=" CA HISAK 18 " ideal model delta sigma weight residual 121.54 133.71 -12.17 1.91e+00 2.74e-01 4.06e+01 angle pdb=" C PROA8 52 " pdb=" N ARGA8 53 " pdb=" CA ARGA8 53 " ideal model delta sigma weight residual 121.54 133.09 -11.55 1.91e+00 2.74e-01 3.66e+01 angle pdb=" C GLYC2 4 " pdb=" N ARGC2 5 " pdb=" CA ARGC2 5 " ideal model delta sigma weight residual 121.70 132.55 -10.85 1.80e+00 3.09e-01 3.64e+01 angle pdb=" C LYSB6 99 " pdb=" N LYSB6 100 " pdb=" CA LYSB6 100 " ideal model delta sigma weight residual 121.80 136.32 -14.52 2.44e+00 1.68e-01 3.54e+01 angle pdb=" N ASPA3 58 " pdb=" CA ASPA3 58 " pdb=" C ASPA3 58 " ideal model delta sigma weight residual 111.02 118.18 -7.16 1.22e+00 6.72e-01 3.44e+01 ... (remaining 52889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.67: 22452 24.67 - 49.35: 889 49.35 - 74.02: 115 74.02 - 98.69: 16 98.69 - 123.37: 1 Dihedral angle restraints: 23473 sinusoidal: 9906 harmonic: 13567 Sorted by residual: dihedral pdb=" CA ALAD5 365 " pdb=" C ALAD5 365 " pdb=" N METD5 366 " pdb=" CA METD5 366 " ideal model delta harmonic sigma weight residual 180.00 -122.93 -57.07 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA PHEB7 30 " pdb=" C PHEB7 30 " pdb=" N PROB7 31 " pdb=" CA PROB7 31 " ideal model delta harmonic sigma weight residual -180.00 -124.06 -55.94 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA METD1 91 " pdb=" C METD1 91 " pdb=" N PROD1 92 " pdb=" CA PROD1 92 " ideal model delta harmonic sigma weight residual -180.00 -127.08 -52.92 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 23470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 5343 0.109 - 0.218: 451 0.218 - 0.328: 21 0.328 - 0.437: 3 0.437 - 0.546: 2 Chirality restraints: 5820 Sorted by residual: chirality pdb=" CG LEUAJ 135 " pdb=" CB LEUAJ 135 " pdb=" CD1 LEUAJ 135 " pdb=" CD2 LEUAJ 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" CA4 CDLD5 904 " pdb=" CA3 CDLD5 904 " pdb=" CA6 CDLD5 904 " pdb=" OA6 CDLD5 904 " both_signs ideal model delta sigma weight residual False -2.57 -2.12 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CB4 CDLB5 201 " pdb=" CB3 CDLB5 201 " pdb=" CB6 CDLB5 201 " pdb=" OB6 CDLB5 201 " both_signs ideal model delta sigma weight residual False -2.57 -2.14 -0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 5817 not shown) Planarity restraints: 6543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHED4 52 " 0.029 2.00e-02 2.50e+03 5.68e-02 3.23e+01 pdb=" C PHED4 52 " -0.098 2.00e-02 2.50e+03 pdb=" O PHED4 52 " 0.037 2.00e-02 2.50e+03 pdb=" N SERD4 53 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHEB7 30 " 0.059 5.00e-02 4.00e+02 9.03e-02 1.30e+01 pdb=" N PROB7 31 " -0.156 5.00e-02 4.00e+02 pdb=" CA PROB7 31 " 0.049 5.00e-02 4.00e+02 pdb=" CD PROB7 31 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYRAJ 206 " 0.035 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYRAJ 206 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYRAJ 206 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYRAJ 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYRAJ 206 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRAJ 206 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYRAJ 206 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYRAJ 206 " 0.006 2.00e-02 2.50e+03 ... (remaining 6540 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4519 2.75 - 3.29: 37469 3.29 - 3.82: 63761 3.82 - 4.36: 71197 4.36 - 4.90: 120781 Nonbonded interactions: 297727 Sorted by model distance: nonbonded pdb=" O LYSB6 86 " pdb=" OG1 THRB6 90 " model vdw 2.212 2.440 nonbonded pdb=" O LEUD4 177 " pdb=" O GLND4 180 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THRAJ 15 " pdb=" OD1 ASPAJ 253 " model vdw 2.240 2.440 nonbonded pdb=" O ALAD1 18 " pdb=" OG1 THRD1 21 " model vdw 2.252 2.440 nonbonded pdb=" OH TYRD4 4 " pdb=" O THRD4 37 " model vdw 2.261 2.440 ... (remaining 297722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 31.170 Check model and map are aligned: 0.550 Set scattering table: 0.360 Process input model: 99.150 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.146 39024 Z= 0.468 Angle : 1.243 16.887 52894 Z= 0.634 Chirality : 0.064 0.546 5820 Planarity : 0.009 0.090 6543 Dihedral : 13.090 123.367 14665 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.31 % Favored : 88.62 % Rotamer: Outliers : 0.27 % Allowed : 6.62 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.32 % Twisted Proline : 2.17 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.10), residues: 4561 helix: -1.81 (0.08), residues: 2795 sheet: -4.14 (0.54), residues: 38 loop : -3.89 (0.12), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRPAM 141 HIS 0.019 0.002 HISAK 18 PHE 0.046 0.003 PHE4L 53 TYR 0.060 0.003 TYRAJ 206 ARG 0.017 0.001 ARGD1 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1860 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1849 time to evaluate : 4.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 36 VAL cc_start: 0.8814 (t) cc_final: 0.8372 (t) REVERT: D3 1 MET cc_start: 0.7021 (pp-130) cc_final: 0.6003 (ppp) REVERT: D3 11 PHE cc_start: 0.8548 (t80) cc_final: 0.8146 (t80) REVERT: D3 89 THR cc_start: 0.9232 (m) cc_final: 0.8821 (p) REVERT: D3 96 PHE cc_start: 0.8156 (t80) cc_final: 0.7850 (t80) REVERT: D1 1 MET cc_start: 0.7587 (mmm) cc_final: 0.7061 (mmm) REVERT: D1 23 VAL cc_start: 0.8511 (t) cc_final: 0.8099 (p) REVERT: D1 25 ARG cc_start: 0.8572 (ttm110) cc_final: 0.8235 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8451 (mmtt) REVERT: D1 81 LEU cc_start: 0.8795 (mt) cc_final: 0.8594 (mp) REVERT: D1 142 TYR cc_start: 0.9349 (m-80) cc_final: 0.9106 (m-10) REVERT: D1 224 PHE cc_start: 0.6982 (t80) cc_final: 0.6681 (t80) REVERT: D1 239 THR cc_start: 0.9093 (m) cc_final: 0.8738 (p) REVERT: D1 271 LEU cc_start: 0.8446 (tm) cc_final: 0.8192 (tm) REVERT: D1 272 TRP cc_start: 0.7404 (t60) cc_final: 0.6782 (t-100) REVERT: D1 279 ARG cc_start: 0.7587 (mtm180) cc_final: 0.7321 (ptt-90) REVERT: D1 281 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.6854 (mpt180) REVERT: D6 15 MET cc_start: 0.7444 (mmm) cc_final: 0.7086 (mmm) REVERT: D6 60 TYR cc_start: 0.5597 (t80) cc_final: 0.5163 (t80) REVERT: D6 70 TYR cc_start: 0.8385 (t80) cc_final: 0.7316 (t80) REVERT: D6 136 PHE cc_start: 0.8543 (p90) cc_final: 0.8086 (p90) REVERT: D6 151 THR cc_start: 0.8329 (p) cc_final: 0.8113 (p) REVERT: D6 155 ILE cc_start: 0.8628 (mt) cc_final: 0.8387 (mt) REVERT: 4L 6 MET cc_start: 0.8720 (tmt) cc_final: 0.8377 (tmm) REVERT: 4L 9 MET cc_start: 0.8466 (mtp) cc_final: 0.8070 (ppp) REVERT: 4L 37 MET cc_start: 0.7334 (ttm) cc_final: 0.6738 (ttm) REVERT: 4L 79 VAL cc_start: 0.9014 (t) cc_final: 0.8712 (p) REVERT: 4L 88 ASP cc_start: 0.8305 (p0) cc_final: 0.7844 (p0) REVERT: D5 119 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8351 (tttp) REVERT: D5 150 MET cc_start: 0.8177 (mmp) cc_final: 0.7671 (mtp) REVERT: D5 279 CYS cc_start: 0.7052 (m) cc_final: 0.6446 (m) REVERT: D5 480 MET cc_start: 0.7175 (tpt) cc_final: 0.6400 (tpp) REVERT: D5 499 ILE cc_start: 0.8718 (mm) cc_final: 0.8398 (mt) REVERT: D5 533 MET cc_start: 0.8568 (mmm) cc_final: 0.8224 (mmt) REVERT: D5 596 LEU cc_start: 0.8778 (mp) cc_final: 0.8520 (tt) REVERT: D4 4 TYR cc_start: 0.6938 (m-10) cc_final: 0.6584 (m-10) REVERT: D4 25 ILE cc_start: 0.8638 (mm) cc_final: 0.8344 (mm) REVERT: D4 108 MET cc_start: 0.7975 (mmp) cc_final: 0.7173 (mmt) REVERT: D4 119 TYR cc_start: 0.8041 (t80) cc_final: 0.7812 (t80) REVERT: D4 178 ILE cc_start: 0.8240 (mt) cc_final: 0.7890 (mm) REVERT: D4 201 MET cc_start: 0.8281 (tpp) cc_final: 0.8036 (ttt) REVERT: D4 225 ILE cc_start: 0.8657 (tp) cc_final: 0.8162 (tp) REVERT: D4 331 ASN cc_start: 0.8952 (t0) cc_final: 0.8712 (t0) REVERT: D4 383 MET cc_start: 0.8828 (mmp) cc_final: 0.8491 (mmp) REVERT: D2 15 LEU cc_start: 0.9124 (tp) cc_final: 0.8905 (tp) REVERT: D2 18 ILE cc_start: 0.8819 (mt) cc_final: 0.8584 (mm) REVERT: D2 36 ASN cc_start: 0.8816 (t160) cc_final: 0.8431 (t0) REVERT: D2 91 ASN cc_start: 0.8637 (t0) cc_final: 0.7944 (t0) REVERT: D2 100 MET cc_start: 0.8894 (mtt) cc_final: 0.8489 (mtp) REVERT: D2 105 LYS cc_start: 0.9107 (tptp) cc_final: 0.8825 (mmmt) REVERT: D2 129 ILE cc_start: 0.9143 (tt) cc_final: 0.8625 (mt) REVERT: D2 154 ILE cc_start: 0.8732 (mt) cc_final: 0.8427 (tp) REVERT: D2 174 GLN cc_start: 0.8712 (mm110) cc_final: 0.8465 (mm-40) REVERT: D2 323 MET cc_start: 0.6848 (mpt) cc_final: 0.6324 (mpt) REVERT: D2 342 ILE cc_start: 0.9249 (mm) cc_final: 0.8787 (mm) REVERT: AK 8 TYR cc_start: 0.9215 (t80) cc_final: 0.8925 (t80) REVERT: AK 33 LEU cc_start: 0.8335 (tt) cc_final: 0.8109 (mt) REVERT: AK 139 LYS cc_start: 0.8298 (pptt) cc_final: 0.8019 (pptt) REVERT: B5 114 MET cc_start: 0.9080 (ttm) cc_final: 0.8831 (ttm) REVERT: AB 77 VAL cc_start: 0.9414 (t) cc_final: 0.9197 (p) REVERT: BJ 16 THR cc_start: 0.8672 (m) cc_final: 0.6709 (m) REVERT: BJ 52 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7114 (mm-30) REVERT: BJ 101 ILE cc_start: 0.9103 (mt) cc_final: 0.8769 (mt) REVERT: BJ 110 LYS cc_start: 0.9276 (mttp) cc_final: 0.8758 (mtmm) REVERT: AJ 131 ASP cc_start: 0.7855 (t0) cc_final: 0.7562 (t0) REVERT: AJ 271 ASN cc_start: 0.8252 (m-40) cc_final: 0.7757 (m110) REVERT: AJ 308 TYR cc_start: 0.8083 (m-80) cc_final: 0.7414 (m-80) REVERT: S5 13 LEU cc_start: 0.8389 (pt) cc_final: 0.8181 (pt) REVERT: S5 14 ASP cc_start: 0.8662 (m-30) cc_final: 0.8414 (m-30) REVERT: S5 16 TRP cc_start: 0.8359 (p-90) cc_final: 0.7790 (p-90) REVERT: S5 64 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7998 (mt-10) REVERT: S5 76 ASN cc_start: 0.8921 (t0) cc_final: 0.8611 (t0) REVERT: A3 45 ASN cc_start: 0.8503 (t0) cc_final: 0.8168 (t0) REVERT: C2 101 PHE cc_start: 0.8332 (m-10) cc_final: 0.8093 (m-10) REVERT: B4 43 LYS cc_start: 0.9286 (mtpm) cc_final: 0.8844 (mmmm) REVERT: B4 65 ILE cc_start: 0.9145 (mm) cc_final: 0.8914 (mt) REVERT: B4 116 GLN cc_start: 0.8586 (tp40) cc_final: 0.8363 (tp-100) REVERT: AM 81 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8182 (tpt170) REVERT: AM 88 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8178 (mt-10) REVERT: AM 96 ILE cc_start: 0.8583 (tt) cc_final: 0.8282 (mt) REVERT: AM 119 MET cc_start: 0.8766 (ptt) cc_final: 0.8440 (ptp) REVERT: AM 136 THR cc_start: 0.8446 (p) cc_final: 0.7664 (p) REVERT: AM 137 TYR cc_start: 0.8193 (m-10) cc_final: 0.7915 (m-10) REVERT: B6 9 LEU cc_start: 0.8332 (tp) cc_final: 0.7751 (tp) REVERT: B6 107 ASP cc_start: 0.8217 (m-30) cc_final: 0.7949 (m-30) REVERT: B6 114 GLU cc_start: 0.7634 (pm20) cc_final: 0.7249 (pm20) REVERT: B7 56 ASP cc_start: 0.8265 (m-30) cc_final: 0.7966 (m-30) REVERT: B7 63 ILE cc_start: 0.9348 (mm) cc_final: 0.9123 (mm) REVERT: B7 85 ASP cc_start: 0.8105 (m-30) cc_final: 0.7829 (m-30) REVERT: B9 79 TYR cc_start: 0.8710 (t80) cc_final: 0.8488 (t80) REVERT: B2 60 THR cc_start: 0.8010 (p) cc_final: 0.7223 (t) REVERT: B8 46 ASP cc_start: 0.8676 (p0) cc_final: 0.8415 (p0) REVERT: B8 72 ASN cc_start: 0.8487 (t0) cc_final: 0.8245 (t0) REVERT: B8 80 ASP cc_start: 0.8644 (m-30) cc_final: 0.8240 (m-30) REVERT: B8 103 LYS cc_start: 0.8445 (mttt) cc_final: 0.8219 (tttp) REVERT: B8 122 TYR cc_start: 0.8318 (m-10) cc_final: 0.8095 (m-10) REVERT: B8 140 LEU cc_start: 0.9167 (mt) cc_final: 0.8623 (mp) REVERT: BK 26 TRP cc_start: 0.7709 (m100) cc_final: 0.7429 (m100) REVERT: BK 83 TYR cc_start: 0.8126 (t80) cc_final: 0.7859 (t80) REVERT: BK 84 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7103 (mmm-85) REVERT: C1 9 HIS cc_start: 0.6995 (p90) cc_final: 0.6186 (p-80) REVERT: C1 41 GLU cc_start: 0.8004 (tp30) cc_final: 0.7595 (tm-30) REVERT: B1 28 ARG cc_start: 0.7141 (mmt180) cc_final: 0.6899 (mtm180) REVERT: A1 28 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7461 (ttp80) REVERT: A1 53 ARG cc_start: 0.8764 (ttm110) cc_final: 0.7692 (ttt-90) outliers start: 11 outliers final: 4 residues processed: 1855 average time/residue: 0.5205 time to fit residues: 1537.2398 Evaluate side-chains 1175 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1171 time to evaluate : 4.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 230 VAL Chi-restraints excluded: chain B8 residue 9 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 378 optimal weight: 2.9990 chunk 339 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 chunk 229 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 351 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 261 optimal weight: 0.0370 chunk 406 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 194 ASN 4L 83 ASN D5 113 ASN D5 116 GLN D5 175 ASN D5 270 ASN ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 509 HIS D5 534 HIS D4 51 ASN D4 139 GLN D4 192 ASN ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 36 ASN D2 63 GLN ** D2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 204 ASN D2 235 ASN D2 316 GLN A8 63 ASN A8 150 ASN A8 162 HIS BJ 130 GLN AJ 21 ASN ** AJ 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 151 HIS AJ 154 GLN AJ 204 ASN AJ 251 GLN AJ 271 ASN ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 6 GLN B4 82 ASN AM 75 GLN AM 89 ASN B6 25 GLN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 32 HIS ** B9 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 104 HIS BK 27 GLN BK 57 ASN A1 27 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 39024 Z= 0.231 Angle : 0.830 12.473 52894 Z= 0.410 Chirality : 0.045 0.307 5820 Planarity : 0.006 0.077 6543 Dihedral : 11.228 120.079 5503 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.45 % Favored : 90.53 % Rotamer: Outliers : 4.50 % Allowed : 17.22 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.32 % Twisted Proline : 1.08 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4561 helix: 0.00 (0.09), residues: 2813 sheet: -3.15 (0.79), residues: 22 loop : -3.58 (0.13), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRPAM 141 HIS 0.018 0.001 HISB9 50 PHE 0.030 0.002 PHED1 104 TYR 0.035 0.002 TYRD5 422 ARG 0.010 0.001 ARGAM 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1320 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8330 (p0) cc_final: 0.8017 (p0) REVERT: D3 11 PHE cc_start: 0.8654 (t80) cc_final: 0.8386 (t80) REVERT: D3 105 GLU cc_start: 0.6554 (tp30) cc_final: 0.6081 (tp30) REVERT: D1 1 MET cc_start: 0.7235 (mmm) cc_final: 0.7025 (mmt) REVERT: D1 23 VAL cc_start: 0.8452 (t) cc_final: 0.8125 (p) REVERT: D1 24 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8060 (tp30) REVERT: D1 25 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8253 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8556 (mmtt) REVERT: D1 30 TYR cc_start: 0.7068 (m-80) cc_final: 0.6794 (m-80) REVERT: D1 100 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8277 (pt) REVERT: D1 195 ARG cc_start: 0.7693 (mtp85) cc_final: 0.7121 (mtm180) REVERT: D1 233 MET cc_start: 0.8701 (tmm) cc_final: 0.8074 (tmm) REVERT: D1 234 MET cc_start: 0.8924 (mmt) cc_final: 0.8305 (mpp) REVERT: D1 251 MET cc_start: 0.7749 (ttp) cc_final: 0.7318 (ptm) REVERT: D1 266 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8591 (tt) REVERT: D1 272 TRP cc_start: 0.7122 (t60) cc_final: 0.6538 (t-100) REVERT: D1 279 ARG cc_start: 0.7712 (mtm180) cc_final: 0.7341 (ptt-90) REVERT: D1 281 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.6851 (mpt180) REVERT: D1 284 GLN cc_start: 0.6971 (mt0) cc_final: 0.6481 (pt0) REVERT: D6 15 MET cc_start: 0.7463 (mmm) cc_final: 0.7047 (mmm) REVERT: D6 70 TYR cc_start: 0.7883 (t80) cc_final: 0.6909 (t80) REVERT: D6 98 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8669 (tm) REVERT: D6 100 GLU cc_start: 0.7005 (tp30) cc_final: 0.6727 (tp30) REVERT: D6 136 PHE cc_start: 0.8540 (p90) cc_final: 0.8223 (p90) REVERT: D6 148 SER cc_start: 0.7215 (p) cc_final: 0.6960 (t) REVERT: 4L 5 TYR cc_start: 0.8227 (m-10) cc_final: 0.7523 (m-80) REVERT: 4L 6 MET cc_start: 0.8959 (tmt) cc_final: 0.8706 (tmm) REVERT: 4L 7 ASN cc_start: 0.8321 (m-40) cc_final: 0.8050 (m-40) REVERT: 4L 36 MET cc_start: 0.8169 (mtp) cc_final: 0.7782 (ttm) REVERT: 4L 37 MET cc_start: 0.7314 (ttm) cc_final: 0.6921 (ttm) REVERT: 4L 47 MET cc_start: 0.8385 (tpp) cc_final: 0.7920 (mmm) REVERT: 4L 79 VAL cc_start: 0.8930 (t) cc_final: 0.8728 (p) REVERT: 4L 88 ASP cc_start: 0.8444 (p0) cc_final: 0.8018 (p0) REVERT: D5 14 LEU cc_start: 0.8847 (mt) cc_final: 0.8296 (mt) REVERT: D5 60 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6575 (mt-10) REVERT: D5 108 MET cc_start: 0.8572 (tpp) cc_final: 0.8247 (mpp) REVERT: D5 381 THR cc_start: 0.8707 (p) cc_final: 0.8040 (t) REVERT: D5 383 MET cc_start: 0.6678 (mmt) cc_final: 0.6358 (mmm) REVERT: D5 393 ASP cc_start: 0.8277 (m-30) cc_final: 0.8062 (m-30) REVERT: D5 397 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7617 (mt-10) REVERT: D5 467 ILE cc_start: 0.8748 (mt) cc_final: 0.8428 (mm) REVERT: D5 480 MET cc_start: 0.7615 (tpt) cc_final: 0.6457 (tpp) REVERT: D5 496 LEU cc_start: 0.8047 (pp) cc_final: 0.7764 (pp) REVERT: D5 533 MET cc_start: 0.8500 (mmm) cc_final: 0.8242 (mmt) REVERT: D4 9 MET cc_start: 0.6980 (ttt) cc_final: 0.6507 (tmm) REVERT: D4 17 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8924 (pp) REVERT: D4 97 SER cc_start: 0.8978 (p) cc_final: 0.8750 (m) REVERT: D4 121 MET cc_start: 0.8293 (mmm) cc_final: 0.7566 (mmm) REVERT: D4 154 LEU cc_start: 0.8831 (tt) cc_final: 0.8523 (tt) REVERT: D4 158 LEU cc_start: 0.9293 (tm) cc_final: 0.8829 (tp) REVERT: D4 200 MET cc_start: 0.8483 (mmt) cc_final: 0.8245 (mmp) REVERT: D4 201 MET cc_start: 0.8230 (tpp) cc_final: 0.8000 (ttt) REVERT: D4 253 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8498 (tp) REVERT: D4 257 MET cc_start: 0.7223 (mmm) cc_final: 0.6415 (mmm) REVERT: D4 263 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7669 (mmt) REVERT: D4 278 ARG cc_start: 0.7859 (ttt-90) cc_final: 0.7488 (ttt-90) REVERT: D4 331 ASN cc_start: 0.9078 (t0) cc_final: 0.8711 (t0) REVERT: D4 379 LEU cc_start: 0.8879 (tt) cc_final: 0.8658 (tp) REVERT: D2 14 MET cc_start: 0.7486 (tmm) cc_final: 0.7039 (tmm) REVERT: D2 15 LEU cc_start: 0.9058 (tp) cc_final: 0.8850 (tp) REVERT: D2 18 ILE cc_start: 0.9054 (mt) cc_final: 0.8817 (mm) REVERT: D2 91 ASN cc_start: 0.8465 (t0) cc_final: 0.7915 (t0) REVERT: D2 105 LYS cc_start: 0.9014 (tptp) cc_final: 0.8603 (mmmt) REVERT: D2 120 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8275 (tp-100) REVERT: D2 129 ILE cc_start: 0.8960 (tt) cc_final: 0.8583 (mt) REVERT: D2 323 MET cc_start: 0.7083 (mpt) cc_final: 0.6476 (mpt) REVERT: AK 8 TYR cc_start: 0.9209 (t80) cc_final: 0.8864 (t80) REVERT: AK 11 ILE cc_start: 0.9100 (mm) cc_final: 0.8810 (mp) REVERT: AK 71 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8746 (tp) REVERT: AK 130 GLU cc_start: 0.7596 (tt0) cc_final: 0.7357 (tt0) REVERT: AK 139 LYS cc_start: 0.8334 (pptt) cc_final: 0.7839 (pptt) REVERT: B5 79 PHE cc_start: 0.8447 (m-10) cc_final: 0.7985 (m-10) REVERT: AB 52 MET cc_start: 0.7951 (tpp) cc_final: 0.7369 (tpp) REVERT: AB 56 ASP cc_start: 0.7204 (m-30) cc_final: 0.6189 (m-30) REVERT: AB 83 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8684 (ttmm) REVERT: A8 47 TRP cc_start: 0.7813 (m100) cc_final: 0.7369 (m100) REVERT: BJ 80 ASP cc_start: 0.8916 (t0) cc_final: 0.8223 (t0) REVERT: BJ 101 ILE cc_start: 0.8876 (mt) cc_final: 0.8590 (mt) REVERT: BJ 110 LYS cc_start: 0.9181 (mttp) cc_final: 0.8774 (mtmm) REVERT: BJ 171 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7763 (mm-30) REVERT: AJ 131 ASP cc_start: 0.7967 (t0) cc_final: 0.7686 (t0) REVERT: AJ 271 ASN cc_start: 0.7948 (m110) cc_final: 0.7647 (m110) REVERT: AJ 308 TYR cc_start: 0.8022 (m-80) cc_final: 0.7491 (m-80) REVERT: AJ 315 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6665 (ttpp) REVERT: S5 16 TRP cc_start: 0.8438 (p-90) cc_final: 0.7921 (p-90) REVERT: S5 41 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7591 (mt-10) REVERT: S5 60 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7689 (mt-10) REVERT: A3 14 LYS cc_start: 0.6582 (mtpt) cc_final: 0.5690 (mttp) REVERT: A3 45 ASN cc_start: 0.8707 (t0) cc_final: 0.8357 (t0) REVERT: B3 33 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8416 (mm-30) REVERT: C2 2 MET cc_start: 0.6369 (ttp) cc_final: 0.6080 (tmm) REVERT: C2 99 GLU cc_start: 0.7898 (pm20) cc_final: 0.7331 (pm20) REVERT: B4 27 GLU cc_start: 0.7847 (pp20) cc_final: 0.7583 (pp20) REVERT: B4 40 SER cc_start: 0.9644 (p) cc_final: 0.8343 (t) REVERT: B4 43 LYS cc_start: 0.9139 (mtpm) cc_final: 0.8674 (ttmm) REVERT: B4 45 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8155 (tm-30) REVERT: B4 47 GLN cc_start: 0.8674 (mt0) cc_final: 0.8085 (mt0) REVERT: B4 116 GLN cc_start: 0.8732 (tp40) cc_final: 0.8529 (tp-100) REVERT: AM 85 MET cc_start: 0.8234 (mmm) cc_final: 0.7716 (mmt) REVERT: AM 93 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7938 (mt-10) REVERT: B6 9 LEU cc_start: 0.8266 (tp) cc_final: 0.7845 (tp) REVERT: B6 13 GLN cc_start: 0.7426 (mp10) cc_final: 0.7205 (mp10) REVERT: B6 107 ASP cc_start: 0.8054 (m-30) cc_final: 0.7698 (m-30) REVERT: B6 121 GLU cc_start: 0.8425 (tt0) cc_final: 0.8217 (tt0) REVERT: B7 85 ASP cc_start: 0.8043 (m-30) cc_final: 0.7805 (m-30) REVERT: B9 83 GLU cc_start: 0.8238 (mp0) cc_final: 0.7964 (mp0) REVERT: B9 123 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8691 (tm-30) REVERT: B8 80 ASP cc_start: 0.8816 (m-30) cc_final: 0.8484 (m-30) REVERT: B8 103 LYS cc_start: 0.8126 (mttt) cc_final: 0.7832 (tttp) REVERT: B8 122 TYR cc_start: 0.8270 (m-10) cc_final: 0.8026 (m-10) REVERT: B8 137 ASN cc_start: 0.8719 (t0) cc_final: 0.8465 (t0) REVERT: C1 5 GLN cc_start: 0.7649 (pp30) cc_final: 0.7065 (pp30) REVERT: C1 9 HIS cc_start: 0.6794 (p90) cc_final: 0.6090 (p-80) REVERT: B1 8 ARG cc_start: 0.5754 (mmp-170) cc_final: 0.4513 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A1 28 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7449 (ttp80) REVERT: A1 53 ARG cc_start: 0.8801 (ttm110) cc_final: 0.7827 (ttt180) outliers start: 184 outliers final: 98 residues processed: 1414 average time/residue: 0.4873 time to fit residues: 1139.1271 Evaluate side-chains 1220 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1112 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D3 residue 72 LEU Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 113 VAL Chi-restraints excluded: chain D1 residue 115 SER Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 46 ASN Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 61 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 132 VAL Chi-restraints excluded: chain D5 residue 163 ASP Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 284 THR Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 341 MET Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 581 LYS Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 120 ILE Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 230 VAL Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 251 ASN Chi-restraints excluded: chain D4 residue 253 ILE Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D2 residue 86 VAL Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 244 VAL Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain AK residue 71 LEU Chi-restraints excluded: chain AK residue 98 LEU Chi-restraints excluded: chain AK residue 114 CYS Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 86 ASN Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 11 ILE Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain A8 residue 11 ASP Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 83 GLU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain BJ residue 82 LEU Chi-restraints excluded: chain BJ residue 103 ASN Chi-restraints excluded: chain AJ residue 16 LYS Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 100 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 159 THR Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 202 ILE Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 24 ILE Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain B4 residue 8 SER Chi-restraints excluded: chain B4 residue 34 GLU Chi-restraints excluded: chain AM residue 95 THR Chi-restraints excluded: chain AM residue 109 VAL Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 90 THR Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 100 GLU Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B2 residue 57 SER Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain B1 residue 7 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 63 SER Chi-restraints excluded: chain A1 residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 226 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 chunk 338 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 407 optimal weight: 0.7980 chunk 440 optimal weight: 0.9990 chunk 362 optimal weight: 2.9990 chunk 404 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 326 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 72 GLN D5 116 GLN D5 332 HIS D4 51 ASN D4 168 GLN ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 99 GLN BJ 133 GLN ** AJ 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 51 ASN B4 125 ASN B9 168 HIS B8 72 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 39024 Z= 0.221 Angle : 0.804 13.188 52894 Z= 0.390 Chirality : 0.045 0.248 5820 Planarity : 0.005 0.070 6543 Dihedral : 10.906 131.338 5503 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.98 % Favored : 90.00 % Rotamer: Outliers : 5.59 % Allowed : 20.50 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 1.08 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.12), residues: 4561 helix: 0.65 (0.10), residues: 2815 sheet: -2.52 (0.83), residues: 22 loop : -3.45 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRPAM 103 HIS 0.015 0.001 HISB9 50 PHE 0.026 0.002 PHE4L 66 TYR 0.030 0.001 TYRD5 422 ARG 0.006 0.000 ARGD5 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1212 time to evaluate : 4.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8566 (p0) cc_final: 0.8202 (p0) REVERT: D3 11 PHE cc_start: 0.8643 (t80) cc_final: 0.8385 (t80) REVERT: D3 88 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8313 (tp) REVERT: D1 23 VAL cc_start: 0.8461 (t) cc_final: 0.8151 (p) REVERT: D1 25 ARG cc_start: 0.8898 (ttm110) cc_final: 0.8145 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8543 (mmtt) REVERT: D1 70 MET cc_start: 0.8702 (tpp) cc_final: 0.8485 (tpp) REVERT: D1 100 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8210 (pt) REVERT: D1 192 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7582 (tm-30) REVERT: D1 195 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6870 (mtm180) REVERT: D1 233 MET cc_start: 0.8620 (tmm) cc_final: 0.8167 (tmm) REVERT: D1 234 MET cc_start: 0.8980 (mmt) cc_final: 0.8620 (mpp) REVERT: D1 251 MET cc_start: 0.7861 (ttp) cc_final: 0.7495 (ptm) REVERT: D1 266 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8583 (tt) REVERT: D1 272 TRP cc_start: 0.7091 (t60) cc_final: 0.6437 (t-100) REVERT: D1 279 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7397 (ptt-90) REVERT: D1 281 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.6803 (mpt180) REVERT: D1 284 GLN cc_start: 0.6960 (mt0) cc_final: 0.6425 (pt0) REVERT: D6 15 MET cc_start: 0.7506 (mmm) cc_final: 0.7041 (mmt) REVERT: D6 70 TYR cc_start: 0.7890 (t80) cc_final: 0.7118 (t80) REVERT: D6 98 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8619 (tm) REVERT: D6 136 PHE cc_start: 0.8623 (p90) cc_final: 0.8140 (p90) REVERT: D6 148 SER cc_start: 0.7359 (p) cc_final: 0.7089 (t) REVERT: 4L 36 MET cc_start: 0.7955 (mtp) cc_final: 0.7474 (ttm) REVERT: 4L 37 MET cc_start: 0.7085 (ttm) cc_final: 0.6787 (ttm) REVERT: 4L 88 ASP cc_start: 0.8491 (p0) cc_final: 0.8017 (p0) REVERT: D5 108 MET cc_start: 0.8584 (tpp) cc_final: 0.8273 (mpp) REVERT: D5 128 MET cc_start: 0.8789 (tpp) cc_final: 0.8245 (tpp) REVERT: D5 154 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9113 (mm) REVERT: D5 380 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8414 (tp) REVERT: D5 381 THR cc_start: 0.8818 (p) cc_final: 0.8143 (t) REVERT: D5 383 MET cc_start: 0.6426 (mmt) cc_final: 0.6128 (mmm) REVERT: D5 397 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7840 (mt-10) REVERT: D5 533 MET cc_start: 0.8426 (mmm) cc_final: 0.8219 (mmt) REVERT: D4 9 MET cc_start: 0.7033 (ttt) cc_final: 0.6488 (tmm) REVERT: D4 17 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8910 (pp) REVERT: D4 108 MET cc_start: 0.8078 (tpp) cc_final: 0.7760 (ttm) REVERT: D4 119 TYR cc_start: 0.9006 (t80) cc_final: 0.8640 (t80) REVERT: D4 121 MET cc_start: 0.8094 (mmm) cc_final: 0.7502 (mmm) REVERT: D4 154 LEU cc_start: 0.8885 (tt) cc_final: 0.8597 (tt) REVERT: D4 158 LEU cc_start: 0.9115 (tm) cc_final: 0.8800 (tp) REVERT: D4 200 MET cc_start: 0.8567 (mmt) cc_final: 0.8353 (mmp) REVERT: D4 201 MET cc_start: 0.8215 (tpp) cc_final: 0.8004 (ttt) REVERT: D4 221 VAL cc_start: 0.8878 (m) cc_final: 0.8490 (p) REVERT: D4 253 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8509 (tp) REVERT: D4 257 MET cc_start: 0.7086 (mmm) cc_final: 0.6424 (mmm) REVERT: D4 263 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7711 (mmt) REVERT: D4 278 ARG cc_start: 0.7942 (ttt-90) cc_final: 0.7549 (ttt-90) REVERT: D4 331 ASN cc_start: 0.9171 (t0) cc_final: 0.8839 (t0) REVERT: D2 14 MET cc_start: 0.7474 (tmm) cc_final: 0.6818 (tmm) REVERT: D2 15 LEU cc_start: 0.9051 (tp) cc_final: 0.8788 (tp) REVERT: D2 18 ILE cc_start: 0.8985 (mt) cc_final: 0.8781 (mm) REVERT: D2 91 ASN cc_start: 0.8455 (t0) cc_final: 0.7866 (t0) REVERT: D2 100 MET cc_start: 0.8856 (mtt) cc_final: 0.8592 (mtp) REVERT: D2 105 LYS cc_start: 0.9038 (tptp) cc_final: 0.8699 (mmmt) REVERT: D2 129 ILE cc_start: 0.8908 (tt) cc_final: 0.8544 (mt) REVERT: D2 158 SER cc_start: 0.8699 (m) cc_final: 0.8445 (p) REVERT: D2 268 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8880 (tm-30) REVERT: D2 313 MET cc_start: 0.7614 (tmm) cc_final: 0.7348 (tmm) REVERT: AK 8 TYR cc_start: 0.9183 (t80) cc_final: 0.8853 (t80) REVERT: AK 114 CYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6282 (t) REVERT: AK 117 MET cc_start: 0.7967 (mmt) cc_final: 0.7493 (mmp) REVERT: AK 130 GLU cc_start: 0.7537 (tt0) cc_final: 0.7305 (tt0) REVERT: AK 139 LYS cc_start: 0.8394 (pptt) cc_final: 0.7878 (pptt) REVERT: B5 79 PHE cc_start: 0.8424 (m-10) cc_final: 0.7836 (m-10) REVERT: B5 114 MET cc_start: 0.8929 (ttm) cc_final: 0.8707 (ttm) REVERT: AB 83 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8700 (ttmm) REVERT: A8 64 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: A8 95 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7950 (mt) REVERT: BJ 80 ASP cc_start: 0.8888 (t0) cc_final: 0.8515 (t0) REVERT: BJ 110 LYS cc_start: 0.9165 (mttp) cc_final: 0.8870 (mtmm) REVERT: AJ 18 MET cc_start: 0.7947 (mmm) cc_final: 0.7445 (mmm) REVERT: AJ 131 ASP cc_start: 0.7878 (t0) cc_final: 0.7598 (t0) REVERT: AJ 271 ASN cc_start: 0.7997 (m110) cc_final: 0.7628 (m110) REVERT: AJ 308 TYR cc_start: 0.7997 (m-80) cc_final: 0.7733 (m-80) REVERT: AJ 315 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6700 (ttpp) REVERT: S5 16 TRP cc_start: 0.8473 (p-90) cc_final: 0.7847 (p-90) REVERT: S5 60 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7582 (mt-10) REVERT: S5 72 MET cc_start: 0.8594 (mtp) cc_final: 0.8390 (mtp) REVERT: A3 45 ASN cc_start: 0.8774 (t0) cc_final: 0.8518 (t0) REVERT: B3 33 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8441 (mm-30) REVERT: C2 2 MET cc_start: 0.6442 (ttp) cc_final: 0.5787 (tmm) REVERT: C2 6 GLN cc_start: 0.5387 (pp30) cc_final: 0.5000 (pp30) REVERT: C2 11 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6798 (pp) REVERT: C2 20 SER cc_start: 0.9000 (m) cc_final: 0.8619 (t) REVERT: C2 109 TYR cc_start: 0.8883 (m-80) cc_final: 0.8518 (m-80) REVERT: B4 40 SER cc_start: 0.9597 (p) cc_final: 0.8222 (t) REVERT: B4 43 LYS cc_start: 0.9109 (mtpm) cc_final: 0.8626 (ttmm) REVERT: B4 45 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B4 47 GLN cc_start: 0.8633 (mt0) cc_final: 0.8225 (mt0) REVERT: B4 116 GLN cc_start: 0.8763 (tp40) cc_final: 0.8460 (tp-100) REVERT: AM 93 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7711 (mt-10) REVERT: B6 31 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.5625 (pp20) REVERT: B6 107 ASP cc_start: 0.8182 (m-30) cc_final: 0.7928 (m-30) REVERT: B6 114 GLU cc_start: 0.7590 (pm20) cc_final: 0.7014 (pm20) REVERT: B6 121 GLU cc_start: 0.8349 (tt0) cc_final: 0.8121 (tt0) REVERT: B7 49 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7323 (tp-100) REVERT: B7 56 ASP cc_start: 0.9076 (p0) cc_final: 0.8701 (p0) REVERT: B7 85 ASP cc_start: 0.8024 (m-30) cc_final: 0.7802 (m-30) REVERT: B9 18 LEU cc_start: 0.8771 (tt) cc_final: 0.8348 (tt) REVERT: B9 67 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B9 79 TYR cc_start: 0.9081 (t80) cc_final: 0.8649 (t80) REVERT: B9 83 GLU cc_start: 0.8197 (mp0) cc_final: 0.7996 (mp0) REVERT: B9 123 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8689 (tm-30) REVERT: B9 134 ARG cc_start: 0.7990 (tmt170) cc_final: 0.7738 (tmm160) REVERT: B2 28 PHE cc_start: 0.8070 (m-80) cc_final: 0.7691 (t80) REVERT: B8 77 MET cc_start: 0.8003 (mtm) cc_final: 0.7753 (ttm) REVERT: B8 80 ASP cc_start: 0.8814 (m-30) cc_final: 0.8499 (m-30) REVERT: B8 103 LYS cc_start: 0.8105 (mttt) cc_final: 0.7847 (tttp) REVERT: B8 122 TYR cc_start: 0.8302 (m-10) cc_final: 0.7843 (m-10) REVERT: B8 137 ASN cc_start: 0.8833 (t0) cc_final: 0.8495 (t0) REVERT: BK 36 ASN cc_start: 0.8800 (t0) cc_final: 0.6286 (t0) REVERT: BK 84 ARG cc_start: 0.7319 (mmm-85) cc_final: 0.6941 (mmt90) REVERT: BK 108 MET cc_start: 0.7740 (ttt) cc_final: 0.7263 (ttt) REVERT: C1 5 GLN cc_start: 0.7585 (pp30) cc_final: 0.7029 (pp30) REVERT: C1 9 HIS cc_start: 0.7045 (p90) cc_final: 0.6760 (p-80) REVERT: B1 8 ARG cc_start: 0.5927 (mmp-170) cc_final: 0.4556 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A1 28 ARG cc_start: 0.7758 (mtp180) cc_final: 0.7436 (ttp80) REVERT: A1 48 MET cc_start: 0.8638 (ttm) cc_final: 0.8123 (ttt) REVERT: A1 53 ARG cc_start: 0.8811 (ttm110) cc_final: 0.7857 (ttt180) outliers start: 229 outliers final: 127 residues processed: 1341 average time/residue: 0.4754 time to fit residues: 1057.0226 Evaluate side-chains 1253 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1109 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D3 residue 2 ASN Chi-restraints excluded: chain D3 residue 7 LEU Chi-restraints excluded: chain D3 residue 17 LEU Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D3 residue 100 VAL Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 53 ILE Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 113 VAL Chi-restraints excluded: chain D1 residue 239 THR Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 46 ASN Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain 4L residue 63 LEU Chi-restraints excluded: chain 4L residue 94 ASN Chi-restraints excluded: chain D5 residue 7 LEU Chi-restraints excluded: chain D5 residue 12 LEU Chi-restraints excluded: chain D5 residue 61 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 132 VAL Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 163 ASP Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 284 THR Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 423 SER Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 590 SER Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 191 SER Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 253 ILE Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 351 LEU Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 441 MET Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 86 VAL Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 117 GLU Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 281 LEU Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 288 LEU Chi-restraints excluded: chain D2 residue 294 MET Chi-restraints excluded: chain D2 residue 295 ARG Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain AK residue 114 CYS Chi-restraints excluded: chain AK residue 120 THR Chi-restraints excluded: chain AK residue 123 LEU Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 41 THR Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 11 ILE Chi-restraints excluded: chain AB residue 40 LEU Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain A8 residue 11 ASP Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 64 GLN Chi-restraints excluded: chain A8 residue 83 GLU Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 166 LEU Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 70 VAL Chi-restraints excluded: chain BJ residue 84 MET Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 100 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 270 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain B4 residue 8 SER Chi-restraints excluded: chain B4 residue 125 ASN Chi-restraints excluded: chain AM residue 109 VAL Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 90 THR Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B9 residue 50 HIS Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B9 residue 161 ASP Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B2 residue 57 SER Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 81 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 77 VAL Chi-restraints excluded: chain BK residue 120 LEU Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 7 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 14 VAL Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 38 VAL Chi-restraints excluded: chain A1 residue 70 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 402 optimal weight: 0.1980 chunk 306 optimal weight: 5.9990 chunk 211 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 273 optimal weight: 5.9990 chunk 409 optimal weight: 0.5980 chunk 433 optimal weight: 0.0270 chunk 213 optimal weight: 0.9980 chunk 387 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN 4L 7 ASN 4L 83 ASN D5 2 ASN ** D4 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 172 GLN D2 289 ASN ** A8 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 84 GLN B7 91 HIS B9 107 HIS B2 58 GLN C1 34 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 39024 Z= 0.200 Angle : 0.779 12.918 52894 Z= 0.377 Chirality : 0.044 0.222 5820 Planarity : 0.005 0.067 6543 Dihedral : 10.351 138.385 5502 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.41 % Favored : 90.57 % Rotamer: Outliers : 5.20 % Allowed : 22.70 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 1.08 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 4561 helix: 0.96 (0.10), residues: 2816 sheet: -2.14 (0.96), residues: 20 loop : -3.32 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRPAM 103 HIS 0.011 0.001 HISD5 328 PHE 0.027 0.002 PHEB6 69 TYR 0.028 0.001 TYRD5 422 ARG 0.005 0.000 ARGD5 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1190 time to evaluate : 4.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8487 (p0) cc_final: 0.8107 (p0) REVERT: D3 11 PHE cc_start: 0.8591 (t80) cc_final: 0.8311 (t80) REVERT: D3 51 PHE cc_start: 0.8501 (p90) cc_final: 0.8105 (p90) REVERT: D3 88 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8566 (tp) REVERT: D1 1 MET cc_start: 0.7715 (mmm) cc_final: 0.7431 (mmt) REVERT: D1 23 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8237 (p) REVERT: D1 25 ARG cc_start: 0.8799 (ttm110) cc_final: 0.8420 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8502 (mmtt) REVERT: D1 73 LEU cc_start: 0.8270 (mt) cc_final: 0.8041 (mm) REVERT: D1 100 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8088 (pt) REVERT: D1 192 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D1 195 ARG cc_start: 0.7503 (mtp85) cc_final: 0.6872 (mtm180) REVERT: D1 233 MET cc_start: 0.8623 (tmm) cc_final: 0.8169 (tmm) REVERT: D1 234 MET cc_start: 0.8898 (mmt) cc_final: 0.8545 (tpp) REVERT: D1 251 MET cc_start: 0.7812 (ttp) cc_final: 0.7538 (ptm) REVERT: D1 266 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8604 (tt) REVERT: D1 272 TRP cc_start: 0.7092 (t60) cc_final: 0.6367 (t-100) REVERT: D1 279 ARG cc_start: 0.7681 (mtm180) cc_final: 0.7344 (ptt-90) REVERT: D1 281 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.6807 (mpt180) REVERT: D1 284 GLN cc_start: 0.6965 (mt0) cc_final: 0.6368 (pt0) REVERT: D6 15 MET cc_start: 0.7460 (mmm) cc_final: 0.7028 (mmt) REVERT: D6 68 PHE cc_start: 0.7846 (m-80) cc_final: 0.7537 (m-80) REVERT: D6 74 MET cc_start: 0.7765 (tpt) cc_final: 0.7299 (tpt) REVERT: D6 98 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8701 (tm) REVERT: D6 136 PHE cc_start: 0.8575 (p90) cc_final: 0.8145 (p90) REVERT: D6 148 SER cc_start: 0.7385 (p) cc_final: 0.7088 (t) REVERT: 4L 88 ASP cc_start: 0.8389 (p0) cc_final: 0.7896 (p0) REVERT: D5 60 GLU cc_start: 0.6918 (mt-10) cc_final: 0.5722 (mt-10) REVERT: D5 154 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9042 (mm) REVERT: D5 277 MET cc_start: 0.8728 (mmm) cc_final: 0.8441 (tpp) REVERT: D5 380 LEU cc_start: 0.8563 (tp) cc_final: 0.8304 (tp) REVERT: D5 393 ASP cc_start: 0.8358 (m-30) cc_final: 0.8117 (m-30) REVERT: D5 397 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7803 (mt-10) REVERT: D5 480 MET cc_start: 0.7644 (tpt) cc_final: 0.6359 (tpp) REVERT: D4 9 MET cc_start: 0.6856 (ttt) cc_final: 0.6494 (tmm) REVERT: D4 17 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8928 (pp) REVERT: D4 104 LEU cc_start: 0.9158 (tt) cc_final: 0.8930 (tp) REVERT: D4 119 TYR cc_start: 0.9083 (t80) cc_final: 0.8146 (t80) REVERT: D4 121 MET cc_start: 0.8061 (mmm) cc_final: 0.7578 (mmm) REVERT: D4 154 LEU cc_start: 0.8921 (tt) cc_final: 0.8665 (tt) REVERT: D4 158 LEU cc_start: 0.9085 (tm) cc_final: 0.8876 (tp) REVERT: D4 221 VAL cc_start: 0.8820 (m) cc_final: 0.8591 (p) REVERT: D4 241 TYR cc_start: 0.8423 (t80) cc_final: 0.8078 (t80) REVERT: D4 257 MET cc_start: 0.7250 (mmm) cc_final: 0.6637 (mmm) REVERT: D4 263 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7683 (mmt) REVERT: D4 278 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7548 (ttt-90) REVERT: D4 297 VAL cc_start: 0.9158 (t) cc_final: 0.8944 (t) REVERT: D4 331 ASN cc_start: 0.9152 (t0) cc_final: 0.8798 (t0) REVERT: D2 14 MET cc_start: 0.7544 (tmm) cc_final: 0.6964 (tmm) REVERT: D2 15 LEU cc_start: 0.9007 (tp) cc_final: 0.8718 (tp) REVERT: D2 91 ASN cc_start: 0.8382 (t0) cc_final: 0.7800 (t0) REVERT: D2 100 MET cc_start: 0.8894 (mtt) cc_final: 0.8642 (mtp) REVERT: D2 105 LYS cc_start: 0.9041 (tptp) cc_final: 0.8624 (mmmt) REVERT: D2 129 ILE cc_start: 0.9196 (tt) cc_final: 0.8843 (mt) REVERT: D2 268 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8758 (tm-30) REVERT: AK 8 TYR cc_start: 0.9051 (t80) cc_final: 0.8843 (t80) REVERT: AK 114 CYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6225 (t) REVERT: AK 117 MET cc_start: 0.7827 (mmt) cc_final: 0.7320 (mmp) REVERT: AK 130 GLU cc_start: 0.7600 (tt0) cc_final: 0.7381 (tt0) REVERT: B5 93 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8891 (mt) REVERT: B5 114 MET cc_start: 0.9017 (ttm) cc_final: 0.8666 (ttm) REVERT: AB 83 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8615 (ttmm) REVERT: A8 95 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8214 (mt) REVERT: BJ 48 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8296 (tpt170) REVERT: BJ 60 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.6034 (t80) REVERT: BJ 98 ASP cc_start: 0.8512 (t0) cc_final: 0.7781 (t0) REVERT: BJ 110 LYS cc_start: 0.9108 (mttp) cc_final: 0.8892 (mtmm) REVERT: BJ 162 MET cc_start: 0.8026 (mtt) cc_final: 0.7762 (mtt) REVERT: AJ 18 MET cc_start: 0.7861 (mmm) cc_final: 0.7324 (mmm) REVERT: AJ 131 ASP cc_start: 0.7810 (t0) cc_final: 0.7593 (t0) REVERT: AJ 271 ASN cc_start: 0.7995 (m110) cc_final: 0.7606 (m110) REVERT: AJ 308 TYR cc_start: 0.7941 (m-80) cc_final: 0.7579 (m-80) REVERT: AJ 315 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6521 (ttmm) REVERT: S5 16 TRP cc_start: 0.8509 (p-90) cc_final: 0.7847 (p-90) REVERT: S5 60 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7617 (mt-10) REVERT: S5 72 MET cc_start: 0.8576 (mtp) cc_final: 0.8373 (mtp) REVERT: A3 19 VAL cc_start: 0.8928 (t) cc_final: 0.8728 (p) REVERT: A3 45 ASN cc_start: 0.8916 (t0) cc_final: 0.8563 (t0) REVERT: B3 29 GLU cc_start: 0.8639 (tt0) cc_final: 0.8364 (mt-10) REVERT: B3 33 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8487 (mm-30) REVERT: C2 2 MET cc_start: 0.6456 (ttp) cc_final: 0.5947 (tmm) REVERT: C2 11 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6860 (pp) REVERT: C2 20 SER cc_start: 0.8908 (m) cc_final: 0.8570 (t) REVERT: C2 109 TYR cc_start: 0.8877 (m-80) cc_final: 0.8432 (m-80) REVERT: B4 40 SER cc_start: 0.9580 (p) cc_final: 0.9028 (t) REVERT: B4 43 LYS cc_start: 0.9083 (mtpm) cc_final: 0.8597 (ttmm) REVERT: B4 45 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B4 47 GLN cc_start: 0.8599 (mt0) cc_final: 0.8255 (mt0) REVERT: B4 74 ASN cc_start: 0.7842 (t0) cc_final: 0.7448 (t0) REVERT: B4 116 GLN cc_start: 0.8793 (tp40) cc_final: 0.8478 (tp-100) REVERT: AM 120 MET cc_start: 0.8435 (tmm) cc_final: 0.8203 (tmm) REVERT: B6 31 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.5377 (pp20) REVERT: B6 96 ILE cc_start: 0.8881 (pt) cc_final: 0.8606 (pt) REVERT: B6 114 GLU cc_start: 0.7552 (pm20) cc_final: 0.7093 (pm20) REVERT: B6 121 GLU cc_start: 0.8177 (tt0) cc_final: 0.7888 (tt0) REVERT: B7 49 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7307 (tp-100) REVERT: B7 56 ASP cc_start: 0.8984 (p0) cc_final: 0.8664 (p0) REVERT: B7 65 PHE cc_start: 0.8415 (t80) cc_final: 0.7949 (t80) REVERT: B7 85 ASP cc_start: 0.8028 (m-30) cc_final: 0.7811 (m-30) REVERT: B9 18 LEU cc_start: 0.8753 (tt) cc_final: 0.8461 (tt) REVERT: B9 27 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7833 (mm-30) REVERT: B9 67 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8148 (mm-30) REVERT: B9 83 GLU cc_start: 0.8096 (mp0) cc_final: 0.7877 (mp0) REVERT: B9 123 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: B9 149 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7672 (ttt180) REVERT: B2 26 GLU cc_start: 0.8624 (tp30) cc_final: 0.8024 (tp30) REVERT: B8 30 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8217 (tpp80) REVERT: B8 58 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7688 (mpp80) REVERT: B8 103 LYS cc_start: 0.8095 (mttt) cc_final: 0.7774 (tttp) REVERT: B8 117 TRP cc_start: 0.8380 (t60) cc_final: 0.7915 (t60) REVERT: B8 122 TYR cc_start: 0.8256 (m-10) cc_final: 0.7803 (m-10) REVERT: B8 137 ASN cc_start: 0.8931 (t0) cc_final: 0.8646 (t0) REVERT: BK 36 ASN cc_start: 0.8908 (t0) cc_final: 0.8537 (t0) REVERT: BK 39 GLU cc_start: 0.8758 (mp0) cc_final: 0.8342 (mp0) REVERT: BK 68 ILE cc_start: 0.8688 (tp) cc_final: 0.8352 (mm) REVERT: C1 5 GLN cc_start: 0.7546 (pp30) cc_final: 0.7011 (pp30) REVERT: C1 9 HIS cc_start: 0.6811 (p90) cc_final: 0.6090 (p-80) REVERT: B1 8 ARG cc_start: 0.5391 (mmp-170) cc_final: 0.4407 (ptp-170) REVERT: B1 26 LEU cc_start: 0.8668 (tt) cc_final: 0.8437 (tt) REVERT: A1 12 MET cc_start: 0.7838 (tmm) cc_final: 0.7566 (tmm) REVERT: A1 16 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8378 (mm) REVERT: A1 28 ARG cc_start: 0.7760 (mtp180) cc_final: 0.7460 (ttp80) REVERT: A1 38 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8764 (p) REVERT: A1 53 ARG cc_start: 0.8760 (ttm110) cc_final: 0.7921 (ttt180) outliers start: 213 outliers final: 129 residues processed: 1289 average time/residue: 0.4721 time to fit residues: 1010.2300 Evaluate side-chains 1250 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1101 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 23 VAL Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 103 LEU Chi-restraints excluded: chain D1 residue 113 VAL Chi-restraints excluded: chain D1 residue 165 LEU Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 54 THR Chi-restraints excluded: chain 4L residue 63 LEU Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain 4L residue 94 ASN Chi-restraints excluded: chain D5 residue 17 MET Chi-restraints excluded: chain D5 residue 61 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 132 VAL Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 163 ASP Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 237 MET Chi-restraints excluded: chain D5 residue 247 LEU Chi-restraints excluded: chain D5 residue 253 VAL Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 536 LEU Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 310 MET Chi-restraints excluded: chain D4 residue 351 LEU Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 410 MET Chi-restraints excluded: chain D2 residue 44 MET Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 117 GLU Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 239 ILE Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 281 LEU Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 294 MET Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain AK residue 114 CYS Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 11 ILE Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 40 LEU Chi-restraints excluded: chain AB residue 85 ASP Chi-restraints excluded: chain AB residue 86 VAL Chi-restraints excluded: chain A8 residue 11 ASP Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 64 GLN Chi-restraints excluded: chain A8 residue 83 GLU Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 166 LEU Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 60 TYR Chi-restraints excluded: chain BJ residue 70 VAL Chi-restraints excluded: chain BJ residue 83 CYS Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 270 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 36 GLU Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain AM residue 109 VAL Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 90 THR Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 58 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain BK residue 60 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain BK residue 77 VAL Chi-restraints excluded: chain C1 residue 34 GLN Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 38 VAL Chi-restraints excluded: chain A1 residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 360 optimal weight: 0.7980 chunk 245 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 322 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 369 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 388 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 235 ASN ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 83 ASN ** D4 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 374 ASN D4 440 HIS ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 18 HIS AJ 92 ASN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B6 13 GLN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 58 GLN B8 72 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39024 Z= 0.230 Angle : 0.784 13.537 52894 Z= 0.379 Chirality : 0.044 0.225 5820 Planarity : 0.005 0.067 6543 Dihedral : 10.052 153.525 5502 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.82 % Favored : 90.16 % Rotamer: Outliers : 5.86 % Allowed : 23.04 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4561 helix: 1.10 (0.10), residues: 2829 sheet: -2.17 (0.97), residues: 20 loop : -3.28 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRPAM 141 HIS 0.022 0.001 HISAK 18 PHE 0.030 0.002 PHED6 47 TYR 0.027 0.001 TYRD1 250 ARG 0.004 0.000 ARGB9 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1153 time to evaluate : 4.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8493 (p0) cc_final: 0.8108 (p0) REVERT: D3 11 PHE cc_start: 0.8611 (t80) cc_final: 0.8317 (t80) REVERT: D1 1 MET cc_start: 0.7827 (mmm) cc_final: 0.7518 (mmt) REVERT: D1 23 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8184 (p) REVERT: D1 25 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8445 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8557 (mmtt) REVERT: D1 70 MET cc_start: 0.8742 (tpp) cc_final: 0.8486 (tpp) REVERT: D1 73 LEU cc_start: 0.8363 (mt) cc_final: 0.8108 (mm) REVERT: D1 100 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7968 (pt) REVERT: D1 156 MET cc_start: 0.8709 (mmt) cc_final: 0.8253 (mmt) REVERT: D1 192 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7576 (tm-30) REVERT: D1 195 ARG cc_start: 0.7469 (mtp85) cc_final: 0.6745 (mtm180) REVERT: D1 233 MET cc_start: 0.8687 (tmm) cc_final: 0.8086 (tmm) REVERT: D1 234 MET cc_start: 0.8945 (mmt) cc_final: 0.8575 (tpp) REVERT: D1 251 MET cc_start: 0.7932 (ttp) cc_final: 0.7679 (ptm) REVERT: D1 266 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8657 (tt) REVERT: D1 271 LEU cc_start: 0.8428 (tm) cc_final: 0.8000 (tm) REVERT: D1 272 TRP cc_start: 0.7138 (t60) cc_final: 0.6425 (t-100) REVERT: D1 279 ARG cc_start: 0.7681 (mtm180) cc_final: 0.7361 (ptt-90) REVERT: D1 281 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.6800 (mpt180) REVERT: D1 284 GLN cc_start: 0.6970 (mt0) cc_final: 0.6373 (pt0) REVERT: D1 317 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D6 90 LEU cc_start: 0.8492 (tt) cc_final: 0.8226 (tt) REVERT: D6 98 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8674 (tm) REVERT: D6 127 ILE cc_start: 0.8827 (pt) cc_final: 0.8444 (pt) REVERT: D6 136 PHE cc_start: 0.8591 (p90) cc_final: 0.8174 (p90) REVERT: D6 148 SER cc_start: 0.7525 (p) cc_final: 0.7215 (t) REVERT: 4L 1 MET cc_start: 0.7053 (ttm) cc_final: 0.6484 (mtm) REVERT: 4L 88 ASP cc_start: 0.8481 (p0) cc_final: 0.7925 (p0) REVERT: D5 1 MET cc_start: 0.7367 (ttm) cc_final: 0.7136 (tpt) REVERT: D5 53 MET cc_start: 0.7777 (tpt) cc_final: 0.7296 (tpt) REVERT: D5 154 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9061 (mm) REVERT: D5 235 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.7944 (t) REVERT: D5 277 MET cc_start: 0.8719 (mmm) cc_final: 0.8426 (tpp) REVERT: D5 397 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7872 (mt-10) REVERT: D5 480 MET cc_start: 0.7529 (tpt) cc_final: 0.6907 (tpp) REVERT: D5 487 LYS cc_start: 0.7742 (ttmp) cc_final: 0.7123 (ttmt) REVERT: D5 511 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6700 (pp) REVERT: D5 544 MET cc_start: 0.7355 (ttt) cc_final: 0.6949 (ttt) REVERT: D4 9 MET cc_start: 0.7300 (ttt) cc_final: 0.6748 (tmm) REVERT: D4 17 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8963 (pp) REVERT: D4 25 ILE cc_start: 0.8666 (mm) cc_final: 0.8381 (mm) REVERT: D4 108 MET cc_start: 0.8390 (ttm) cc_final: 0.8141 (ttm) REVERT: D4 119 TYR cc_start: 0.8940 (t80) cc_final: 0.8278 (t80) REVERT: D4 121 MET cc_start: 0.8013 (mmm) cc_final: 0.7672 (tpp) REVERT: D4 123 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7052 (mt-10) REVERT: D4 141 GLU cc_start: 0.8407 (pm20) cc_final: 0.8082 (pp20) REVERT: D4 152 TYR cc_start: 0.8362 (m-80) cc_final: 0.8162 (m-80) REVERT: D4 154 LEU cc_start: 0.9078 (tt) cc_final: 0.8752 (tt) REVERT: D4 171 MET cc_start: 0.8520 (tmm) cc_final: 0.8289 (tmm) REVERT: D4 221 VAL cc_start: 0.8784 (m) cc_final: 0.8518 (p) REVERT: D4 222 GLU cc_start: 0.8043 (tt0) cc_final: 0.7510 (tt0) REVERT: D4 241 TYR cc_start: 0.8558 (t80) cc_final: 0.8247 (t80) REVERT: D4 257 MET cc_start: 0.7168 (mmm) cc_final: 0.6937 (mmm) REVERT: D4 263 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7772 (mmt) REVERT: D4 331 ASN cc_start: 0.9134 (t0) cc_final: 0.8921 (t0) REVERT: D2 14 MET cc_start: 0.7536 (tmm) cc_final: 0.6940 (tmm) REVERT: D2 15 LEU cc_start: 0.8976 (tp) cc_final: 0.8705 (tp) REVERT: D2 91 ASN cc_start: 0.8516 (t0) cc_final: 0.7926 (t0) REVERT: D2 104 MET cc_start: 0.8803 (ttm) cc_final: 0.8305 (ttm) REVERT: D2 105 LYS cc_start: 0.9026 (tptp) cc_final: 0.8594 (mmmt) REVERT: D2 129 ILE cc_start: 0.9223 (tt) cc_final: 0.8880 (mt) REVERT: D2 268 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8896 (tm-30) REVERT: AK 8 TYR cc_start: 0.9188 (t80) cc_final: 0.8861 (t80) REVERT: AK 22 TYR cc_start: 0.8181 (t80) cc_final: 0.7957 (t80) REVERT: AK 114 CYS cc_start: 0.6469 (OUTLIER) cc_final: 0.6087 (t) REVERT: AK 117 MET cc_start: 0.7665 (mmt) cc_final: 0.7129 (mmp) REVERT: AK 126 MET cc_start: 0.8218 (mmt) cc_final: 0.7930 (mmt) REVERT: AK 130 GLU cc_start: 0.7692 (tt0) cc_final: 0.7085 (tt0) REVERT: B5 45 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8851 (t) REVERT: B5 93 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8876 (mt) REVERT: B5 112 ARG cc_start: 0.8454 (ptm160) cc_final: 0.8199 (ptm160) REVERT: B5 114 MET cc_start: 0.9001 (ttm) cc_final: 0.8685 (ttm) REVERT: AB 52 MET cc_start: 0.8001 (tpt) cc_final: 0.7559 (tpt) REVERT: AB 54 MET cc_start: 0.8677 (mmp) cc_final: 0.8418 (mmp) REVERT: AB 64 ASP cc_start: 0.8144 (m-30) cc_final: 0.7702 (t70) REVERT: AB 83 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8627 (ttmm) REVERT: BJ 48 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8403 (tpt170) REVERT: BJ 60 TYR cc_start: 0.6414 (m-80) cc_final: 0.6183 (t80) REVERT: BJ 80 ASP cc_start: 0.8467 (t0) cc_final: 0.8098 (t0) REVERT: AJ 18 MET cc_start: 0.8011 (mmm) cc_final: 0.7487 (mmm) REVERT: AJ 131 ASP cc_start: 0.7877 (t0) cc_final: 0.7672 (t0) REVERT: AJ 271 ASN cc_start: 0.8045 (m110) cc_final: 0.7625 (m110) REVERT: AJ 308 TYR cc_start: 0.7998 (m-80) cc_final: 0.7410 (m-80) REVERT: AJ 315 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6490 (ttmm) REVERT: S5 60 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7790 (mt-10) REVERT: S5 91 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6338 (p90) REVERT: A3 14 LYS cc_start: 0.6761 (mtpt) cc_final: 0.5878 (mttp) REVERT: A3 45 ASN cc_start: 0.8960 (t0) cc_final: 0.8690 (t0) REVERT: C2 2 MET cc_start: 0.6387 (ttp) cc_final: 0.5733 (tmm) REVERT: C2 11 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7096 (pp) REVERT: C2 80 ASP cc_start: 0.8304 (t0) cc_final: 0.8078 (t0) REVERT: C2 109 TYR cc_start: 0.8894 (m-80) cc_final: 0.8442 (m-80) REVERT: B4 27 GLU cc_start: 0.8038 (pp20) cc_final: 0.7604 (tm-30) REVERT: B4 43 LYS cc_start: 0.9150 (mtpm) cc_final: 0.8727 (ttmm) REVERT: B4 45 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8126 (tm-30) REVERT: B4 47 GLN cc_start: 0.8602 (mt0) cc_final: 0.8262 (mt0) REVERT: B4 74 ASN cc_start: 0.8151 (t0) cc_final: 0.7693 (t0) REVERT: B4 116 GLN cc_start: 0.8747 (tp40) cc_final: 0.8444 (tp-100) REVERT: B4 125 ASN cc_start: 0.8015 (t0) cc_final: 0.7666 (m-40) REVERT: AM 85 MET cc_start: 0.8083 (mmt) cc_final: 0.7781 (mmt) REVERT: B6 31 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5329 (pp20) REVERT: B6 96 ILE cc_start: 0.8816 (pt) cc_final: 0.8580 (pt) REVERT: B6 114 GLU cc_start: 0.7622 (pm20) cc_final: 0.7059 (pm20) REVERT: B7 49 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7258 (tp-100) REVERT: B7 56 ASP cc_start: 0.9044 (p0) cc_final: 0.8792 (p0) REVERT: B7 65 PHE cc_start: 0.8463 (t80) cc_final: 0.8004 (t80) REVERT: B9 67 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8174 (mm-30) REVERT: B2 26 GLU cc_start: 0.8600 (tp30) cc_final: 0.8078 (tp30) REVERT: B8 58 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7788 (mpp80) REVERT: B8 77 MET cc_start: 0.7809 (ttm) cc_final: 0.7459 (ttm) REVERT: B8 103 LYS cc_start: 0.8067 (mttt) cc_final: 0.7798 (tttp) REVERT: B8 122 TYR cc_start: 0.8297 (m-10) cc_final: 0.7807 (m-10) REVERT: B8 137 ASN cc_start: 0.8909 (t0) cc_final: 0.8650 (t0) REVERT: BK 36 ASN cc_start: 0.8880 (t0) cc_final: 0.8419 (t0) REVERT: BK 68 ILE cc_start: 0.8581 (tp) cc_final: 0.8187 (mm) REVERT: BK 108 MET cc_start: 0.7311 (ttt) cc_final: 0.6958 (ttt) REVERT: C1 5 GLN cc_start: 0.7561 (pp30) cc_final: 0.7036 (pp30) REVERT: C1 9 HIS cc_start: 0.6890 (p90) cc_final: 0.6154 (p-80) REVERT: B1 8 ARG cc_start: 0.6028 (mmp-170) cc_final: 0.4824 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8265 (mm) REVERT: A1 28 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7519 (ttp80) REVERT: A1 34 ARG cc_start: 0.8266 (mmt90) cc_final: 0.7967 (mmt-90) outliers start: 240 outliers final: 167 residues processed: 1279 average time/residue: 0.4632 time to fit residues: 986.2120 Evaluate side-chains 1275 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1089 time to evaluate : 4.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 17 LEU Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 23 VAL Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 103 LEU Chi-restraints excluded: chain D1 residue 113 VAL Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 165 LEU Chi-restraints excluded: chain D1 residue 183 MET Chi-restraints excluded: chain D1 residue 235 ASN Chi-restraints excluded: chain D1 residue 239 THR Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 122 MET Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 54 THR Chi-restraints excluded: chain 4L residue 63 LEU Chi-restraints excluded: chain 4L residue 69 CYS Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain 4L residue 94 ASN Chi-restraints excluded: chain D5 residue 12 LEU Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 132 VAL Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 155 ILE Chi-restraints excluded: chain D5 residue 163 ASP Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 235 SER Chi-restraints excluded: chain D5 residue 237 MET Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 276 ILE Chi-restraints excluded: chain D5 residue 284 THR Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 381 THR Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 511 LEU Chi-restraints excluded: chain D5 residue 590 SER Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 78 MET Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 191 SER Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 235 LEU Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 351 LEU Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 403 THR Chi-restraints excluded: chain D4 residue 410 MET Chi-restraints excluded: chain D4 residue 441 MET Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 44 MET Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 117 GLU Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 281 LEU Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 294 MET Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 320 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 331 VAL Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain AK residue 114 CYS Chi-restraints excluded: chain AK residue 123 LEU Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 45 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 11 ILE Chi-restraints excluded: chain AB residue 19 LEU Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 40 LEU Chi-restraints excluded: chain AB residue 85 ASP Chi-restraints excluded: chain AB residue 86 VAL Chi-restraints excluded: chain A8 residue 11 ASP Chi-restraints excluded: chain A8 residue 15 GLN Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 55 CYS Chi-restraints excluded: chain A8 residue 64 GLN Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 70 VAL Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 83 CYS Chi-restraints excluded: chain BJ residue 132 THR Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 92 ASN Chi-restraints excluded: chain AJ residue 100 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain B4 residue 8 SER Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain AM residue 32 TYR Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 90 THR Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 9 LEU Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B9 residue 161 ASP Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 58 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 60 VAL Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain BK residue 77 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 38 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 145 optimal weight: 0.7980 chunk 389 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 254 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 433 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 chunk 200 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D3 108 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 235 ASN ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN 4L 7 ASN 4L 83 ASN D4 44 GLN D4 51 ASN ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 97 GLN ** S5 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 77 GLN B2 13 GLN C1 34 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39024 Z= 0.218 Angle : 0.789 14.277 52894 Z= 0.380 Chirality : 0.044 0.246 5820 Planarity : 0.005 0.066 6543 Dihedral : 9.745 137.972 5502 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.52 % Favored : 90.44 % Rotamer: Outliers : 5.67 % Allowed : 24.43 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4561 helix: 1.24 (0.10), residues: 2816 sheet: -2.11 (1.01), residues: 20 loop : -3.21 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRPAM 103 HIS 0.030 0.001 HISB9 50 PHE 0.029 0.002 PHE4L 41 TYR 0.033 0.001 TYRD1 250 ARG 0.008 0.000 ARGBK 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1155 time to evaluate : 4.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 29 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8168 (tmtt) REVERT: S2 34 ASN cc_start: 0.8482 (p0) cc_final: 0.8037 (p0) REVERT: D3 51 PHE cc_start: 0.8371 (p90) cc_final: 0.7994 (p90) REVERT: D1 23 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8238 (p) REVERT: D1 25 ARG cc_start: 0.8816 (ttm110) cc_final: 0.8235 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8641 (mptt) REVERT: D1 70 MET cc_start: 0.8733 (tpp) cc_final: 0.8422 (tpp) REVERT: D1 100 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8002 (pt) REVERT: D1 192 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7558 (tm-30) REVERT: D1 195 ARG cc_start: 0.7465 (mtp85) cc_final: 0.6809 (mtm180) REVERT: D1 233 MET cc_start: 0.8661 (tmm) cc_final: 0.7974 (tmm) REVERT: D1 234 MET cc_start: 0.8968 (mmt) cc_final: 0.8649 (tpp) REVERT: D1 251 MET cc_start: 0.7962 (ttp) cc_final: 0.7658 (ptm) REVERT: D1 266 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8502 (tt) REVERT: D1 271 LEU cc_start: 0.8375 (tm) cc_final: 0.8065 (tm) REVERT: D1 272 TRP cc_start: 0.7195 (t60) cc_final: 0.6408 (t-100) REVERT: D1 279 ARG cc_start: 0.7674 (mtm180) cc_final: 0.7383 (ptt-90) REVERT: D1 281 ARG cc_start: 0.8152 (ttp-170) cc_final: 0.6608 (mpt180) REVERT: D1 284 GLN cc_start: 0.6979 (mt0) cc_final: 0.6345 (pt0) REVERT: D1 317 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7866 (tm-30) REVERT: D6 68 PHE cc_start: 0.7859 (m-80) cc_final: 0.7493 (m-80) REVERT: D6 90 LEU cc_start: 0.8472 (tt) cc_final: 0.8210 (tt) REVERT: D6 98 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8632 (tm) REVERT: D6 114 GLU cc_start: 0.7857 (tt0) cc_final: 0.7380 (pm20) REVERT: D6 120 ASN cc_start: 0.7312 (t0) cc_final: 0.6858 (t0) REVERT: D6 127 ILE cc_start: 0.8748 (pt) cc_final: 0.8533 (pt) REVERT: D6 136 PHE cc_start: 0.8568 (p90) cc_final: 0.8304 (p90) REVERT: D6 148 SER cc_start: 0.7409 (p) cc_final: 0.7111 (t) REVERT: 4L 1 MET cc_start: 0.7342 (ttm) cc_final: 0.6979 (mtm) REVERT: 4L 88 ASP cc_start: 0.8486 (p0) cc_final: 0.7932 (p0) REVERT: D5 53 MET cc_start: 0.7859 (tpt) cc_final: 0.7583 (tpt) REVERT: D5 87 MET cc_start: 0.8052 (tpp) cc_final: 0.7580 (tpp) REVERT: D5 108 MET cc_start: 0.8440 (mmt) cc_final: 0.7887 (tpp) REVERT: D5 154 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8988 (mm) REVERT: D5 277 MET cc_start: 0.8669 (mmm) cc_final: 0.8405 (tpp) REVERT: D5 393 ASP cc_start: 0.8289 (m-30) cc_final: 0.7986 (m-30) REVERT: D5 397 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7799 (mt-10) REVERT: D5 487 LYS cc_start: 0.7730 (ttmp) cc_final: 0.7086 (ttmt) REVERT: D5 544 MET cc_start: 0.7496 (ttt) cc_final: 0.7079 (ttt) REVERT: D4 9 MET cc_start: 0.7261 (ttt) cc_final: 0.6778 (tmm) REVERT: D4 17 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8970 (pp) REVERT: D4 25 ILE cc_start: 0.8643 (mm) cc_final: 0.8396 (mm) REVERT: D4 108 MET cc_start: 0.8578 (ttm) cc_final: 0.8099 (ttm) REVERT: D4 119 TYR cc_start: 0.8895 (t80) cc_final: 0.8179 (t80) REVERT: D4 123 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6762 (mt-10) REVERT: D4 141 GLU cc_start: 0.8400 (pm20) cc_final: 0.8166 (pp20) REVERT: D4 152 TYR cc_start: 0.8427 (m-80) cc_final: 0.8140 (m-80) REVERT: D4 154 LEU cc_start: 0.9108 (tt) cc_final: 0.8750 (tt) REVERT: D4 171 MET cc_start: 0.8565 (tmm) cc_final: 0.8323 (tmm) REVERT: D4 221 VAL cc_start: 0.8800 (m) cc_final: 0.8524 (p) REVERT: D4 222 GLU cc_start: 0.8051 (tt0) cc_final: 0.7362 (tt0) REVERT: D4 241 TYR cc_start: 0.8610 (t80) cc_final: 0.8147 (t80) REVERT: D4 257 MET cc_start: 0.7177 (mmm) cc_final: 0.6968 (mmm) REVERT: D4 263 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7725 (mmt) REVERT: D4 331 ASN cc_start: 0.9126 (t0) cc_final: 0.8905 (t0) REVERT: D4 378 GLU cc_start: 0.7666 (tt0) cc_final: 0.6918 (tt0) REVERT: D4 400 MET cc_start: 0.7478 (tpp) cc_final: 0.7152 (tpp) REVERT: D2 14 MET cc_start: 0.7511 (tmm) cc_final: 0.7152 (tmm) REVERT: D2 91 ASN cc_start: 0.8454 (t0) cc_final: 0.7870 (t0) REVERT: D2 104 MET cc_start: 0.8868 (ttm) cc_final: 0.8315 (ttm) REVERT: D2 105 LYS cc_start: 0.9015 (tptp) cc_final: 0.8578 (mmmt) REVERT: D2 129 ILE cc_start: 0.9230 (tt) cc_final: 0.8870 (mt) REVERT: D2 268 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8959 (tm-30) REVERT: AK 8 TYR cc_start: 0.9211 (t80) cc_final: 0.8891 (t80) REVERT: AK 22 TYR cc_start: 0.8124 (t80) cc_final: 0.7881 (t80) REVERT: AK 114 CYS cc_start: 0.6438 (OUTLIER) cc_final: 0.6057 (t) REVERT: AK 117 MET cc_start: 0.7601 (mmt) cc_final: 0.7113 (mmp) REVERT: AK 130 GLU cc_start: 0.7682 (tt0) cc_final: 0.7041 (tt0) REVERT: B5 45 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8861 (t) REVERT: B5 93 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8840 (mt) REVERT: B5 114 MET cc_start: 0.8996 (ttm) cc_final: 0.8673 (ttm) REVERT: AB 52 MET cc_start: 0.7965 (tpt) cc_final: 0.7475 (tpt) REVERT: AB 54 MET cc_start: 0.8762 (mmp) cc_final: 0.8514 (mmp) REVERT: AB 64 ASP cc_start: 0.8041 (m-30) cc_final: 0.7689 (t70) REVERT: AB 71 MET cc_start: 0.7517 (tpp) cc_final: 0.7117 (tpp) REVERT: AB 83 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8455 (ttmm) REVERT: A8 95 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8126 (mt) REVERT: BJ 16 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8139 (p) REVERT: BJ 48 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8504 (tpt170) REVERT: BJ 80 ASP cc_start: 0.8364 (t0) cc_final: 0.7960 (t0) REVERT: BJ 89 MET cc_start: 0.8630 (mmp) cc_final: 0.8214 (mmt) REVERT: AJ 18 MET cc_start: 0.7963 (mmm) cc_final: 0.7492 (mmm) REVERT: AJ 131 ASP cc_start: 0.8084 (t0) cc_final: 0.7865 (t0) REVERT: AJ 271 ASN cc_start: 0.8058 (m110) cc_final: 0.7629 (m110) REVERT: AJ 308 TYR cc_start: 0.7969 (m-80) cc_final: 0.7438 (m-80) REVERT: AJ 315 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.6325 (ttmm) REVERT: S5 23 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7057 (mm-30) REVERT: S5 60 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7783 (mt-10) REVERT: S5 91 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6340 (p90) REVERT: A3 45 ASN cc_start: 0.9005 (t0) cc_final: 0.8613 (t0) REVERT: C2 2 MET cc_start: 0.6242 (ttp) cc_final: 0.5868 (tmm) REVERT: C2 11 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7084 (pp) REVERT: C2 80 ASP cc_start: 0.8307 (t0) cc_final: 0.7969 (t0) REVERT: C2 109 TYR cc_start: 0.8920 (m-80) cc_final: 0.8432 (m-80) REVERT: B4 27 GLU cc_start: 0.8003 (pp20) cc_final: 0.7678 (tm-30) REVERT: B4 40 SER cc_start: 0.9495 (p) cc_final: 0.9201 (t) REVERT: B4 43 LYS cc_start: 0.9153 (mtpm) cc_final: 0.8787 (ttmm) REVERT: B4 47 GLN cc_start: 0.8486 (mt0) cc_final: 0.8178 (mt0) REVERT: B4 74 ASN cc_start: 0.8150 (t0) cc_final: 0.7742 (t0) REVERT: B4 116 GLN cc_start: 0.8757 (tp40) cc_final: 0.8482 (tp-100) REVERT: B4 124 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.5799 (p90) REVERT: B4 125 ASN cc_start: 0.8016 (t0) cc_final: 0.7744 (m-40) REVERT: AM 85 MET cc_start: 0.8077 (mmt) cc_final: 0.7734 (mmt) REVERT: B6 14 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9028 (tp) REVERT: B6 31 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5360 (pp20) REVERT: B6 96 ILE cc_start: 0.8771 (pt) cc_final: 0.8533 (pt) REVERT: B6 114 GLU cc_start: 0.7658 (pm20) cc_final: 0.7163 (pm20) REVERT: B7 49 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7292 (tp-100) REVERT: B7 56 ASP cc_start: 0.8890 (p0) cc_final: 0.8604 (p0) REVERT: B2 26 GLU cc_start: 0.8591 (tp30) cc_final: 0.8108 (tp30) REVERT: B8 68 ASP cc_start: 0.7473 (t70) cc_final: 0.7261 (t70) REVERT: B8 71 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8760 (mp) REVERT: B8 77 MET cc_start: 0.7843 (ttm) cc_final: 0.7442 (ttm) REVERT: B8 90 ASP cc_start: 0.7172 (p0) cc_final: 0.6837 (p0) REVERT: B8 103 LYS cc_start: 0.8107 (mttt) cc_final: 0.7783 (tttp) REVERT: B8 122 TYR cc_start: 0.8289 (m-10) cc_final: 0.7768 (m-10) REVERT: B8 137 ASN cc_start: 0.8920 (t0) cc_final: 0.8662 (t0) REVERT: BK 36 ASN cc_start: 0.8729 (t0) cc_final: 0.8500 (t0) REVERT: BK 68 ILE cc_start: 0.8672 (tp) cc_final: 0.8331 (mm) REVERT: BK 108 MET cc_start: 0.7119 (ttt) cc_final: 0.6909 (ttt) REVERT: C1 5 GLN cc_start: 0.7561 (pp30) cc_final: 0.7019 (pp30) REVERT: C1 9 HIS cc_start: 0.6879 (p90) cc_final: 0.6151 (p-80) REVERT: C1 34 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: B1 8 ARG cc_start: 0.5884 (mmp-170) cc_final: 0.4744 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8395 (mm) REVERT: A1 28 ARG cc_start: 0.7790 (mtp180) cc_final: 0.7512 (ttp80) REVERT: A1 34 ARG cc_start: 0.8350 (mmt90) cc_final: 0.7813 (mmt90) outliers start: 232 outliers final: 166 residues processed: 1279 average time/residue: 0.4671 time to fit residues: 994.8409 Evaluate side-chains 1271 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1083 time to evaluate : 4.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 17 LEU Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 23 VAL Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 165 LEU Chi-restraints excluded: chain D1 residue 183 MET Chi-restraints excluded: chain D1 residue 235 ASN Chi-restraints excluded: chain D1 residue 239 THR Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 122 MET Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 151 THR Chi-restraints excluded: chain D6 residue 161 LEU Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 54 THR Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain 4L residue 76 SER Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain 4L residue 94 ASN Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 78 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 132 VAL Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 163 ASP Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 217 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 237 MET Chi-restraints excluded: chain D5 residue 251 THR Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 276 ILE Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 381 THR Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 590 SER Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 78 MET Chi-restraints excluded: chain D4 residue 97 SER Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 191 SER Chi-restraints excluded: chain D4 residue 195 MET Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 351 LEU Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 441 MET Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 117 GLU Chi-restraints excluded: chain D2 residue 145 ILE Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 281 LEU Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 294 MET Chi-restraints excluded: chain D2 residue 296 LEU Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 320 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain AK residue 114 CYS Chi-restraints excluded: chain AK residue 123 LEU Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 45 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 11 ILE Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 40 LEU Chi-restraints excluded: chain AB residue 85 ASP Chi-restraints excluded: chain A8 residue 11 ASP Chi-restraints excluded: chain A8 residue 15 GLN Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 35 CYS Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 55 CYS Chi-restraints excluded: chain A8 residue 64 GLN Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 144 ARG Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 83 CYS Chi-restraints excluded: chain BJ residue 132 THR Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 100 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 159 THR Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 14 ASP Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain B4 residue 8 SER Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain B4 residue 124 PHE Chi-restraints excluded: chain AM residue 68 ILE Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 110 LEU Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 9 LEU Chi-restraints excluded: chain B9 residue 42 LEU Chi-restraints excluded: chain B9 residue 77 GLN Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B2 residue 7 ILE Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain BK residue 77 VAL Chi-restraints excluded: chain C1 residue 34 GLN Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 38 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 417 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 364 optimal weight: 0.5980 chunk 242 optimal weight: 4.9990 chunk 431 optimal weight: 0.0370 chunk 270 optimal weight: 4.9990 chunk 263 optimal weight: 0.1980 chunk 199 optimal weight: 0.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 235 ASN ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN D5 226 GLN D4 51 ASN ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 68 HIS A3 70 GLN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 77 GLN B2 13 GLN B2 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39024 Z= 0.230 Angle : 0.804 14.134 52894 Z= 0.386 Chirality : 0.044 0.222 5820 Planarity : 0.005 0.075 6543 Dihedral : 9.598 136.964 5502 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.78 % Favored : 90.20 % Rotamer: Outliers : 5.89 % Allowed : 24.95 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4561 helix: 1.29 (0.10), residues: 2800 sheet: -2.13 (0.98), residues: 20 loop : -3.12 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRPAM 103 HIS 0.016 0.001 HISB9 50 PHE 0.025 0.002 PHEB6 69 TYR 0.033 0.001 TYRD1 250 ARG 0.016 0.000 ARGD5 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1123 time to evaluate : 4.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 29 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8171 (tmtt) REVERT: S2 34 ASN cc_start: 0.8384 (p0) cc_final: 0.7960 (p0) REVERT: D3 11 PHE cc_start: 0.8138 (t80) cc_final: 0.7882 (t80) REVERT: D3 51 PHE cc_start: 0.8307 (p90) cc_final: 0.7911 (p90) REVERT: D1 23 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8237 (p) REVERT: D1 25 ARG cc_start: 0.8827 (ttm110) cc_final: 0.8214 (ttm-80) REVERT: D1 26 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8504 (mmpt) REVERT: D1 70 MET cc_start: 0.8722 (tpp) cc_final: 0.8209 (tpp) REVERT: D1 97 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8167 (p0) REVERT: D1 100 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8055 (pt) REVERT: D1 192 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7493 (tm-30) REVERT: D1 195 ARG cc_start: 0.7502 (mtp85) cc_final: 0.6845 (mtm180) REVERT: D1 251 MET cc_start: 0.7938 (ttp) cc_final: 0.7472 (ptm) REVERT: D1 266 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8510 (tt) REVERT: D1 271 LEU cc_start: 0.8300 (tm) cc_final: 0.7994 (tm) REVERT: D1 272 TRP cc_start: 0.7212 (t60) cc_final: 0.6420 (t-100) REVERT: D1 279 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7370 (ptt-90) REVERT: D1 281 ARG cc_start: 0.8064 (ttp-170) cc_final: 0.6578 (mpt180) REVERT: D1 284 GLN cc_start: 0.6932 (mt0) cc_final: 0.6356 (pt0) REVERT: D1 317 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7888 (tm-30) REVERT: D6 98 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8637 (tm) REVERT: D6 114 GLU cc_start: 0.7815 (tt0) cc_final: 0.7375 (pm20) REVERT: D6 120 ASN cc_start: 0.7269 (t0) cc_final: 0.6856 (t0) REVERT: D6 136 PHE cc_start: 0.8579 (p90) cc_final: 0.8200 (p90) REVERT: D6 148 SER cc_start: 0.7555 (p) cc_final: 0.7308 (t) REVERT: 4L 1 MET cc_start: 0.7238 (ttm) cc_final: 0.6976 (mtm) REVERT: 4L 17 THR cc_start: 0.8925 (m) cc_final: 0.8442 (p) REVERT: 4L 88 ASP cc_start: 0.8483 (p0) cc_final: 0.7949 (p0) REVERT: D5 7 LEU cc_start: 0.8665 (mm) cc_final: 0.8328 (mt) REVERT: D5 86 SER cc_start: 0.8827 (m) cc_final: 0.8453 (t) REVERT: D5 87 MET cc_start: 0.8006 (tpp) cc_final: 0.7454 (tpp) REVERT: D5 150 MET cc_start: 0.8695 (tpp) cc_final: 0.8443 (mmp) REVERT: D5 154 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8973 (mm) REVERT: D5 341 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6846 (ttt) REVERT: D5 393 ASP cc_start: 0.8305 (m-30) cc_final: 0.8000 (m-30) REVERT: D5 397 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7771 (mt-10) REVERT: D5 487 LYS cc_start: 0.7697 (ttmp) cc_final: 0.7081 (ttmt) REVERT: D5 544 MET cc_start: 0.7659 (ttt) cc_final: 0.7229 (ttt) REVERT: D5 573 MET cc_start: 0.7823 (mtp) cc_final: 0.7196 (mtp) REVERT: D4 9 MET cc_start: 0.7261 (ttt) cc_final: 0.6573 (tmm) REVERT: D4 17 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9005 (pp) REVERT: D4 25 ILE cc_start: 0.8619 (mm) cc_final: 0.8391 (mm) REVERT: D4 44 GLN cc_start: 0.8227 (pt0) cc_final: 0.7736 (pt0) REVERT: D4 108 MET cc_start: 0.8490 (ttm) cc_final: 0.8011 (ttm) REVERT: D4 119 TYR cc_start: 0.8902 (t80) cc_final: 0.8337 (t80) REVERT: D4 123 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6779 (mt-10) REVERT: D4 154 LEU cc_start: 0.9147 (tt) cc_final: 0.8916 (tt) REVERT: D4 171 MET cc_start: 0.8499 (tmm) cc_final: 0.8279 (tmm) REVERT: D4 221 VAL cc_start: 0.8842 (m) cc_final: 0.8423 (p) REVERT: D4 241 TYR cc_start: 0.8561 (t80) cc_final: 0.8353 (t80) REVERT: D4 263 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7764 (mmt) REVERT: D4 331 ASN cc_start: 0.9124 (t0) cc_final: 0.8870 (t0) REVERT: D4 378 GLU cc_start: 0.7631 (tt0) cc_final: 0.7020 (tt0) REVERT: D4 400 MET cc_start: 0.7574 (tpp) cc_final: 0.7233 (tpp) REVERT: D4 437 MET cc_start: 0.8272 (mmp) cc_final: 0.7826 (mmt) REVERT: D2 14 MET cc_start: 0.7628 (tmm) cc_final: 0.7107 (tmm) REVERT: D2 15 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7753 (mp) REVERT: D2 68 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7272 (tpp) REVERT: D2 91 ASN cc_start: 0.8478 (t0) cc_final: 0.7925 (t0) REVERT: D2 104 MET cc_start: 0.8908 (ttm) cc_final: 0.8343 (ttm) REVERT: D2 105 LYS cc_start: 0.9004 (tptp) cc_final: 0.8555 (mmmt) REVERT: D2 129 ILE cc_start: 0.8949 (tt) cc_final: 0.8599 (mt) REVERT: D2 130 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7708 (pp) REVERT: D2 266 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8796 (mt) REVERT: D2 268 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8917 (tm-30) REVERT: AK 8 TYR cc_start: 0.9161 (t80) cc_final: 0.8898 (t80) REVERT: AK 114 CYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6095 (t) REVERT: AK 117 MET cc_start: 0.7556 (mmt) cc_final: 0.7083 (mmp) REVERT: AK 130 GLU cc_start: 0.7706 (tt0) cc_final: 0.7113 (tt0) REVERT: B5 45 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.8920 (t) REVERT: B5 93 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8785 (mt) REVERT: B5 114 MET cc_start: 0.8967 (ttm) cc_final: 0.8578 (ttm) REVERT: AB 52 MET cc_start: 0.7927 (tpt) cc_final: 0.7460 (tpt) REVERT: AB 64 ASP cc_start: 0.8089 (m-30) cc_final: 0.7708 (t70) REVERT: AB 83 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8152 (ttmm) REVERT: A8 95 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8166 (mt) REVERT: BJ 16 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8151 (p) REVERT: BJ 48 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8464 (tpt170) REVERT: AJ 18 MET cc_start: 0.7951 (mmm) cc_final: 0.7455 (mmm) REVERT: AJ 315 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6421 (ttmm) REVERT: S5 23 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7126 (mm-30) REVERT: S5 60 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7739 (mt-10) REVERT: S5 91 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.6267 (p90) REVERT: A3 45 ASN cc_start: 0.9030 (t0) cc_final: 0.8613 (t0) REVERT: B3 29 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8143 (mt-10) REVERT: C2 2 MET cc_start: 0.6229 (ttp) cc_final: 0.5887 (tmm) REVERT: C2 11 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7001 (pp) REVERT: C2 80 ASP cc_start: 0.8325 (t0) cc_final: 0.7961 (t0) REVERT: C2 109 TYR cc_start: 0.8930 (m-80) cc_final: 0.8416 (m-80) REVERT: B4 27 GLU cc_start: 0.7954 (pp20) cc_final: 0.7621 (tm-30) REVERT: B4 40 SER cc_start: 0.9500 (p) cc_final: 0.9215 (t) REVERT: B4 43 LYS cc_start: 0.9164 (mtpm) cc_final: 0.8739 (ttmm) REVERT: B4 47 GLN cc_start: 0.8477 (mt0) cc_final: 0.8151 (mt0) REVERT: B4 74 ASN cc_start: 0.8033 (t0) cc_final: 0.7600 (t0) REVERT: B4 116 GLN cc_start: 0.8757 (tp40) cc_final: 0.8515 (tp-100) REVERT: B4 124 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.6069 (p90) REVERT: B6 14 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9020 (tp) REVERT: B6 31 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5494 (pp20) REVERT: B7 49 GLN cc_start: 0.8308 (tp-100) cc_final: 0.7283 (tp-100) REVERT: B7 56 ASP cc_start: 0.8873 (p0) cc_final: 0.8624 (p0) REVERT: B7 102 GLU cc_start: 0.8407 (tp30) cc_final: 0.7211 (tp30) REVERT: B9 27 GLU cc_start: 0.8067 (tp30) cc_final: 0.7855 (mm-30) REVERT: B9 67 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8378 (mm-30) REVERT: B2 26 GLU cc_start: 0.8545 (tp30) cc_final: 0.8118 (tp30) REVERT: B8 58 ARG cc_start: 0.8314 (mpp80) cc_final: 0.8029 (mpp80) REVERT: B8 71 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8763 (mp) REVERT: B8 77 MET cc_start: 0.7840 (ttm) cc_final: 0.7480 (ttm) REVERT: B8 90 ASP cc_start: 0.6952 (p0) cc_final: 0.6570 (p0) REVERT: B8 103 LYS cc_start: 0.8094 (mttt) cc_final: 0.7769 (tttp) REVERT: B8 122 TYR cc_start: 0.8298 (m-10) cc_final: 0.7799 (m-10) REVERT: BK 25 ARG cc_start: 0.8485 (tpp80) cc_final: 0.8231 (tpp80) REVERT: BK 68 ILE cc_start: 0.8672 (tp) cc_final: 0.8318 (mm) REVERT: BK 83 TYR cc_start: 0.7487 (t80) cc_final: 0.7131 (t80) REVERT: C1 5 GLN cc_start: 0.7564 (pp30) cc_final: 0.7006 (pp30) REVERT: C1 34 GLN cc_start: 0.8537 (tt0) cc_final: 0.8169 (tt0) REVERT: B1 8 ARG cc_start: 0.5862 (mmp-170) cc_final: 0.4694 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8374 (mm) REVERT: A1 28 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7504 (ttp80) REVERT: A1 34 ARG cc_start: 0.8500 (mmt90) cc_final: 0.7987 (mmt90) outliers start: 241 outliers final: 178 residues processed: 1245 average time/residue: 0.5066 time to fit residues: 1065.7840 Evaluate side-chains 1288 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1083 time to evaluate : 5.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 7 LEU Chi-restraints excluded: chain D3 residue 88 LEU Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 23 VAL Chi-restraints excluded: chain D1 residue 97 ASN Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 165 LEU Chi-restraints excluded: chain D1 residue 183 MET Chi-restraints excluded: chain D1 residue 235 ASN Chi-restraints excluded: chain D1 residue 239 THR Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D1 residue 306 SER Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 46 ASN Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 122 MET Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain D6 residue 151 THR Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 54 THR Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain 4L residue 76 SER Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain 4L residue 94 ASN Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 61 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 78 LEU Chi-restraints excluded: chain D5 residue 100 ILE Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 155 ILE Chi-restraints excluded: chain D5 residue 163 ASP Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 237 MET Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 251 THR Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 259 LEU Chi-restraints excluded: chain D5 residue 276 ILE Chi-restraints excluded: chain D5 residue 329 ILE Chi-restraints excluded: chain D5 residue 341 MET Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 381 THR Chi-restraints excluded: chain D5 residue 383 MET Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 590 SER Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 62 SER Chi-restraints excluded: chain D4 residue 78 MET Chi-restraints excluded: chain D4 residue 122 PHE Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 191 SER Chi-restraints excluded: chain D4 residue 195 MET Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 235 LEU Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 351 LEU Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 403 THR Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 15 LEU Chi-restraints excluded: chain D2 residue 68 MET Chi-restraints excluded: chain D2 residue 69 LEU Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 117 GLU Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 145 ILE Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 202 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 320 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain AK residue 114 CYS Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 45 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain AB residue 8 LEU Chi-restraints excluded: chain AB residue 11 ILE Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 40 LEU Chi-restraints excluded: chain AB residue 85 ASP Chi-restraints excluded: chain A8 residue 11 ASP Chi-restraints excluded: chain A8 residue 15 GLN Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 35 CYS Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 55 CYS Chi-restraints excluded: chain A8 residue 64 GLN Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 60 TYR Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 83 CYS Chi-restraints excluded: chain BJ residue 98 ASP Chi-restraints excluded: chain BJ residue 132 THR Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 100 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 159 THR Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 5 VAL Chi-restraints excluded: chain S5 residue 14 ASP Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain C2 residue 75 LEU Chi-restraints excluded: chain B4 residue 8 SER Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain B4 residue 124 PHE Chi-restraints excluded: chain AM residue 32 TYR Chi-restraints excluded: chain AM residue 68 ILE Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 9 LEU Chi-restraints excluded: chain B9 residue 42 LEU Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B9 residue 161 ASP Chi-restraints excluded: chain B2 residue 7 ILE Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 53 ARG Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain BK residue 77 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 267 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 274 optimal weight: 0.8980 chunk 294 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 339 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN 4L 7 ASN ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 141 GLN ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 77 GLN B2 13 GLN B2 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39024 Z= 0.238 Angle : 0.820 12.464 52894 Z= 0.394 Chirality : 0.045 0.220 5820 Planarity : 0.005 0.067 6543 Dihedral : 9.491 134.031 5502 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.89 % Favored : 90.09 % Rotamer: Outliers : 5.52 % Allowed : 26.04 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4561 helix: 1.28 (0.10), residues: 2807 sheet: -2.12 (0.99), residues: 20 loop : -3.11 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRPB4 100 HIS 0.017 0.001 HISB9 50 PHE 0.032 0.002 PHE4L 66 TYR 0.046 0.001 TYRB9 90 ARG 0.013 0.000 ARGD5 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1124 time to evaluate : 4.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 29 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8175 (tmtt) REVERT: S2 34 ASN cc_start: 0.8378 (p0) cc_final: 0.7959 (p0) REVERT: D3 51 PHE cc_start: 0.8262 (p90) cc_final: 0.7930 (p90) REVERT: D1 25 ARG cc_start: 0.8834 (ttm110) cc_final: 0.8223 (ttm-80) REVERT: D1 100 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8083 (pt) REVERT: D1 156 MET cc_start: 0.8699 (mmt) cc_final: 0.8329 (mmt) REVERT: D1 192 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7542 (tm-30) REVERT: D1 195 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7042 (mtp180) REVERT: D1 235 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8431 (t0) REVERT: D1 251 MET cc_start: 0.7928 (ttp) cc_final: 0.7436 (ptm) REVERT: D1 272 TRP cc_start: 0.7230 (t60) cc_final: 0.6433 (t-100) REVERT: D1 279 ARG cc_start: 0.7660 (mtm180) cc_final: 0.7403 (ptt-90) REVERT: D1 284 GLN cc_start: 0.6831 (mt0) cc_final: 0.6465 (pt0) REVERT: D1 317 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D6 2 MET cc_start: 0.5350 (tpp) cc_final: 0.5078 (mmt) REVERT: D6 98 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8631 (tm) REVERT: D6 114 GLU cc_start: 0.7779 (tt0) cc_final: 0.7379 (pm20) REVERT: D6 120 ASN cc_start: 0.7445 (t0) cc_final: 0.7062 (t0) REVERT: D6 136 PHE cc_start: 0.8585 (p90) cc_final: 0.8234 (p90) REVERT: D6 148 SER cc_start: 0.7586 (p) cc_final: 0.7311 (t) REVERT: 4L 17 THR cc_start: 0.8874 (m) cc_final: 0.8391 (p) REVERT: D5 7 LEU cc_start: 0.8662 (mm) cc_final: 0.8388 (mt) REVERT: D5 86 SER cc_start: 0.8828 (m) cc_final: 0.8447 (t) REVERT: D5 87 MET cc_start: 0.8040 (tpp) cc_final: 0.7454 (tpp) REVERT: D5 150 MET cc_start: 0.8766 (tpp) cc_final: 0.8477 (mmp) REVERT: D5 154 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8952 (mm) REVERT: D5 341 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6877 (ttt) REVERT: D5 393 ASP cc_start: 0.8290 (m-30) cc_final: 0.8047 (m-30) REVERT: D5 397 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7845 (mt-10) REVERT: D5 487 LYS cc_start: 0.7546 (ttmp) cc_final: 0.7156 (ttmt) REVERT: D5 573 MET cc_start: 0.7715 (mtp) cc_final: 0.7295 (mtp) REVERT: D4 9 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6590 (tmm) REVERT: D4 17 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9047 (pp) REVERT: D4 25 ILE cc_start: 0.8635 (mm) cc_final: 0.8406 (mm) REVERT: D4 44 GLN cc_start: 0.8206 (pt0) cc_final: 0.7772 (pt0) REVERT: D4 119 TYR cc_start: 0.8984 (t80) cc_final: 0.8407 (t80) REVERT: D4 123 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7182 (mt-10) REVERT: D4 141 GLU cc_start: 0.8384 (pm20) cc_final: 0.7814 (pp20) REVERT: D4 171 MET cc_start: 0.8557 (tmm) cc_final: 0.8323 (tmm) REVERT: D4 204 MET cc_start: 0.8738 (mmt) cc_final: 0.8361 (mpp) REVERT: D4 221 VAL cc_start: 0.8881 (m) cc_final: 0.8551 (p) REVERT: D4 229 MET cc_start: 0.8345 (mtp) cc_final: 0.8127 (mtm) REVERT: D4 241 TYR cc_start: 0.8604 (t80) cc_final: 0.8321 (t80) REVERT: D4 257 MET cc_start: 0.6735 (mmm) cc_final: 0.6415 (mmm) REVERT: D4 263 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7766 (mmt) REVERT: D4 294 MET cc_start: 0.8773 (mmm) cc_final: 0.8497 (mmp) REVERT: D4 325 MET cc_start: 0.7555 (ttp) cc_final: 0.6553 (ttp) REVERT: D4 378 GLU cc_start: 0.7589 (tt0) cc_final: 0.6996 (tt0) REVERT: D4 400 MET cc_start: 0.7529 (tpp) cc_final: 0.7130 (tpp) REVERT: D4 437 MET cc_start: 0.8164 (mmp) cc_final: 0.7835 (mmt) REVERT: D2 14 MET cc_start: 0.7650 (tmm) cc_final: 0.7257 (tmm) REVERT: D2 91 ASN cc_start: 0.8523 (t0) cc_final: 0.7947 (t0) REVERT: D2 104 MET cc_start: 0.8924 (ttm) cc_final: 0.8363 (ttm) REVERT: D2 105 LYS cc_start: 0.8961 (tptp) cc_final: 0.8517 (mmmt) REVERT: D2 129 ILE cc_start: 0.8953 (tt) cc_final: 0.8609 (mt) REVERT: D2 130 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7710 (pp) REVERT: D2 171 ASN cc_start: 0.6809 (t0) cc_final: 0.6514 (t0) REVERT: D2 268 GLN cc_start: 0.9344 (tm-30) cc_final: 0.8953 (tm-30) REVERT: AK 8 TYR cc_start: 0.9178 (t80) cc_final: 0.8888 (t80) REVERT: AK 114 CYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6106 (t) REVERT: AK 117 MET cc_start: 0.7512 (mmt) cc_final: 0.7087 (mmp) REVERT: AK 130 GLU cc_start: 0.7786 (tt0) cc_final: 0.7089 (tt0) REVERT: B5 45 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.8944 (t) REVERT: B5 93 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8821 (mt) REVERT: B5 114 MET cc_start: 0.8957 (ttm) cc_final: 0.8651 (ttm) REVERT: AB 52 MET cc_start: 0.7877 (tpt) cc_final: 0.7391 (tpt) REVERT: AB 64 ASP cc_start: 0.8111 (m-30) cc_final: 0.7714 (t70) REVERT: AB 83 LYS cc_start: 0.8780 (ttmm) cc_final: 0.7903 (ttmm) REVERT: A8 34 GLN cc_start: 0.7777 (tp-100) cc_final: 0.7523 (tp-100) REVERT: A8 95 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8289 (mt) REVERT: BJ 16 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8147 (p) REVERT: BJ 48 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8506 (tpt170) REVERT: BJ 60 TYR cc_start: 0.6175 (OUTLIER) cc_final: 0.5903 (t80) REVERT: BJ 84 MET cc_start: 0.7550 (mtt) cc_final: 0.7088 (mtt) REVERT: AJ 18 MET cc_start: 0.8046 (mmm) cc_final: 0.7528 (mmm) REVERT: AJ 131 ASP cc_start: 0.7557 (t0) cc_final: 0.7324 (t0) REVERT: AJ 315 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6385 (ttmm) REVERT: S5 23 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7121 (mm-30) REVERT: S5 60 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7754 (mt-10) REVERT: S5 76 ASN cc_start: 0.8759 (t0) cc_final: 0.8557 (t0) REVERT: S5 91 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6231 (p90) REVERT: A3 45 ASN cc_start: 0.9064 (t0) cc_final: 0.8632 (t0) REVERT: C2 2 MET cc_start: 0.6256 (ttp) cc_final: 0.6050 (tmm) REVERT: C2 11 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6911 (pp) REVERT: C2 80 ASP cc_start: 0.8326 (t0) cc_final: 0.8101 (t0) REVERT: C2 109 TYR cc_start: 0.8959 (m-80) cc_final: 0.8246 (m-80) REVERT: B4 27 GLU cc_start: 0.7973 (pp20) cc_final: 0.7642 (tm-30) REVERT: B4 40 SER cc_start: 0.9534 (p) cc_final: 0.9233 (t) REVERT: B4 43 LYS cc_start: 0.9134 (mtpm) cc_final: 0.8761 (ttmm) REVERT: B4 47 GLN cc_start: 0.8483 (mt0) cc_final: 0.8148 (mt0) REVERT: B4 74 ASN cc_start: 0.7955 (t0) cc_final: 0.7599 (t0) REVERT: B4 116 GLN cc_start: 0.8750 (tp40) cc_final: 0.8523 (tp-100) REVERT: B4 124 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.6116 (p90) REVERT: B4 128 TYR cc_start: 0.7920 (p90) cc_final: 0.7669 (p90) REVERT: AM 97 MET cc_start: 0.8571 (ttt) cc_final: 0.8293 (tmm) REVERT: B6 14 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9049 (tp) REVERT: B6 31 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5490 (pp20) REVERT: B7 49 GLN cc_start: 0.8259 (tp-100) cc_final: 0.7255 (tp-100) REVERT: B7 102 GLU cc_start: 0.8584 (tp30) cc_final: 0.8286 (tp30) REVERT: B9 18 LEU cc_start: 0.8779 (tt) cc_final: 0.8400 (tt) REVERT: B9 67 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B2 26 GLU cc_start: 0.8529 (tp30) cc_final: 0.8125 (tp30) REVERT: B8 58 ARG cc_start: 0.8292 (mpp80) cc_final: 0.7866 (mpp80) REVERT: B8 71 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8812 (mp) REVERT: B8 77 MET cc_start: 0.7891 (ttm) cc_final: 0.7515 (ttm) REVERT: B8 90 ASP cc_start: 0.6995 (p0) cc_final: 0.6609 (p0) REVERT: B8 103 LYS cc_start: 0.8090 (mttt) cc_final: 0.7775 (tttp) REVERT: B8 122 TYR cc_start: 0.8360 (m-10) cc_final: 0.7880 (m-10) REVERT: BK 25 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8176 (tpp80) REVERT: BK 68 ILE cc_start: 0.8689 (tp) cc_final: 0.8353 (mm) REVERT: BK 83 TYR cc_start: 0.7560 (t80) cc_final: 0.7199 (t80) REVERT: C1 5 GLN cc_start: 0.7568 (pp30) cc_final: 0.6964 (pp30) REVERT: B1 8 ARG cc_start: 0.5881 (mmp-170) cc_final: 0.4703 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A1 28 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7524 (ttp80) REVERT: A1 34 ARG cc_start: 0.8582 (mmt90) cc_final: 0.8298 (mmt-90) outliers start: 226 outliers final: 177 residues processed: 1234 average time/residue: 0.4571 time to fit residues: 941.7401 Evaluate side-chains 1275 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1074 time to evaluate : 4.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 7 LEU Chi-restraints excluded: chain D3 residue 81 THR Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 165 LEU Chi-restraints excluded: chain D1 residue 183 MET Chi-restraints excluded: chain D1 residue 235 ASN Chi-restraints excluded: chain D1 residue 239 THR Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 102 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 122 MET Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain D6 residue 151 THR Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 54 THR Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain 4L residue 76 SER Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain 4L residue 94 ASN Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 17 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 69 LEU Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 163 ASP Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 217 ILE Chi-restraints excluded: chain D5 residue 233 LEU Chi-restraints excluded: chain D5 residue 237 MET Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 251 THR Chi-restraints excluded: chain D5 residue 254 VAL Chi-restraints excluded: chain D5 residue 276 ILE Chi-restraints excluded: chain D5 residue 341 MET Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 381 THR Chi-restraints excluded: chain D5 residue 383 MET Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 590 SER Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 9 MET Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 62 SER Chi-restraints excluded: chain D4 residue 78 MET Chi-restraints excluded: chain D4 residue 97 SER Chi-restraints excluded: chain D4 residue 106 LEU Chi-restraints excluded: chain D4 residue 122 PHE Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 191 SER Chi-restraints excluded: chain D4 residue 195 MET Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 264 LEU Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 351 LEU Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 44 MET Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 117 GLU Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 145 ILE Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 202 LEU Chi-restraints excluded: chain D2 residue 205 LEU Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 320 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain AK residue 114 CYS Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 45 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain B5 residue 110 VAL Chi-restraints excluded: chain AB residue 8 LEU Chi-restraints excluded: chain AB residue 11 ILE Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 40 LEU Chi-restraints excluded: chain AB residue 85 ASP Chi-restraints excluded: chain A8 residue 11 ASP Chi-restraints excluded: chain A8 residue 15 GLN Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 35 CYS Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 64 GLN Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 60 TYR Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 83 CYS Chi-restraints excluded: chain BJ residue 98 ASP Chi-restraints excluded: chain BJ residue 132 THR Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 100 LEU Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 159 THR Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 5 VAL Chi-restraints excluded: chain S5 residue 14 ASP Chi-restraints excluded: chain S5 residue 54 GLU Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 43 LEU Chi-restraints excluded: chain C2 residue 65 ILE Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain C2 residue 69 VAL Chi-restraints excluded: chain B4 residue 8 SER Chi-restraints excluded: chain B4 residue 25 SER Chi-restraints excluded: chain B4 residue 64 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 87 LEU Chi-restraints excluded: chain B4 residue 124 PHE Chi-restraints excluded: chain AM residue 32 TYR Chi-restraints excluded: chain AM residue 68 ILE Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B6 residue 115 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 9 LEU Chi-restraints excluded: chain B9 residue 42 LEU Chi-restraints excluded: chain B9 residue 47 PHE Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B9 residue 161 ASP Chi-restraints excluded: chain B2 residue 7 ILE Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 71 VAL Chi-restraints excluded: chain BK residue 77 VAL Chi-restraints excluded: chain C1 residue 39 VAL Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 38 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 392 optimal weight: 0.0770 chunk 413 optimal weight: 0.4980 chunk 377 optimal weight: 0.5980 chunk 402 optimal weight: 0.9980 chunk 242 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 363 optimal weight: 0.5980 chunk 380 optimal weight: 0.7980 chunk 400 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 89 ASN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 77 GLN B2 13 GLN B2 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39024 Z= 0.217 Angle : 0.827 14.798 52894 Z= 0.395 Chirality : 0.045 0.223 5820 Planarity : 0.005 0.064 6543 Dihedral : 9.346 134.027 5502 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.52 % Favored : 90.46 % Rotamer: Outliers : 4.91 % Allowed : 26.68 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4561 helix: 1.33 (0.10), residues: 2788 sheet: -1.92 (1.05), residues: 20 loop : -3.09 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRPB4 100 HIS 0.013 0.001 HISD5 328 PHE 0.027 0.002 PHE4L 66 TYR 0.048 0.001 TYRB9 90 ARG 0.011 0.000 ARGD5 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1131 time to evaluate : 4.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 34 ASN cc_start: 0.8369 (p0) cc_final: 0.7959 (p0) REVERT: D1 25 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8293 (ttm-80) REVERT: D1 100 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7985 (pt) REVERT: D1 192 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7503 (tm-30) REVERT: D1 195 ARG cc_start: 0.7430 (mtp85) cc_final: 0.7034 (mtp180) REVERT: D1 233 MET cc_start: 0.8530 (tmm) cc_final: 0.7694 (tmm) REVERT: D1 234 MET cc_start: 0.9008 (mmt) cc_final: 0.8574 (mpp) REVERT: D1 240 THR cc_start: 0.9206 (t) cc_final: 0.8856 (t) REVERT: D1 251 MET cc_start: 0.7912 (ttp) cc_final: 0.7518 (ptm) REVERT: D1 266 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8518 (tt) REVERT: D1 272 TRP cc_start: 0.7117 (t60) cc_final: 0.6306 (t-100) REVERT: D1 284 GLN cc_start: 0.6952 (mt0) cc_final: 0.6498 (pt0) REVERT: D1 317 GLN cc_start: 0.8311 (tm-30) cc_final: 0.8026 (tm-30) REVERT: D6 2 MET cc_start: 0.5349 (tpp) cc_final: 0.5094 (mmt) REVERT: D6 98 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8617 (tm) REVERT: D6 114 GLU cc_start: 0.7774 (tt0) cc_final: 0.7375 (pm20) REVERT: D6 136 PHE cc_start: 0.8559 (p90) cc_final: 0.8180 (p90) REVERT: D6 148 SER cc_start: 0.7571 (p) cc_final: 0.7365 (t) REVERT: 4L 1 MET cc_start: 0.6860 (mtm) cc_final: 0.6639 (ptm) REVERT: 4L 17 THR cc_start: 0.9041 (m) cc_final: 0.8698 (p) REVERT: D5 7 LEU cc_start: 0.8801 (mm) cc_final: 0.8433 (mt) REVERT: D5 66 TRP cc_start: 0.8156 (t60) cc_final: 0.7924 (t60) REVERT: D5 86 SER cc_start: 0.8843 (m) cc_final: 0.8430 (t) REVERT: D5 87 MET cc_start: 0.7914 (tpp) cc_final: 0.7351 (tpp) REVERT: D5 150 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8442 (mmp) REVERT: D5 154 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8890 (mm) REVERT: D5 393 ASP cc_start: 0.8262 (m-30) cc_final: 0.7995 (m-30) REVERT: D5 544 MET cc_start: 0.7775 (ttt) cc_final: 0.7464 (ttt) REVERT: D5 573 MET cc_start: 0.7642 (mtp) cc_final: 0.7400 (mtp) REVERT: D4 9 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6711 (tmm) REVERT: D4 17 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9028 (pp) REVERT: D4 25 ILE cc_start: 0.8554 (mm) cc_final: 0.8336 (mm) REVERT: D4 44 GLN cc_start: 0.7966 (pt0) cc_final: 0.7585 (pt0) REVERT: D4 119 TYR cc_start: 0.8901 (t80) cc_final: 0.8428 (t80) REVERT: D4 123 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7248 (mt-10) REVERT: D4 141 GLU cc_start: 0.8370 (pm20) cc_final: 0.7762 (pp20) REVERT: D4 171 MET cc_start: 0.8529 (tmm) cc_final: 0.8279 (tmm) REVERT: D4 204 MET cc_start: 0.8665 (mmt) cc_final: 0.8315 (mpp) REVERT: D4 241 TYR cc_start: 0.8612 (t80) cc_final: 0.8318 (t80) REVERT: D4 257 MET cc_start: 0.6683 (mmm) cc_final: 0.6404 (mmm) REVERT: D4 263 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7694 (mmt) REVERT: D4 294 MET cc_start: 0.8678 (mmm) cc_final: 0.8198 (mmm) REVERT: D4 325 MET cc_start: 0.7609 (ttp) cc_final: 0.7143 (ttp) REVERT: D4 378 GLU cc_start: 0.7572 (tt0) cc_final: 0.6954 (tt0) REVERT: D4 400 MET cc_start: 0.7510 (tpp) cc_final: 0.7117 (tpp) REVERT: D2 14 MET cc_start: 0.7644 (tmm) cc_final: 0.7259 (tmm) REVERT: D2 68 MET cc_start: 0.7217 (ttm) cc_final: 0.6824 (ttt) REVERT: D2 91 ASN cc_start: 0.8503 (t0) cc_final: 0.7925 (t0) REVERT: D2 105 LYS cc_start: 0.8964 (tptp) cc_final: 0.8503 (mmmt) REVERT: D2 129 ILE cc_start: 0.8921 (tt) cc_final: 0.8588 (mt) REVERT: D2 130 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7636 (pp) REVERT: D2 171 ASN cc_start: 0.6484 (t0) cc_final: 0.6220 (t0) REVERT: D2 190 MET cc_start: 0.8523 (ttm) cc_final: 0.7306 (ttm) REVERT: D2 268 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8650 (tm-30) REVERT: D2 313 MET cc_start: 0.7810 (ttp) cc_final: 0.7544 (ppp) REVERT: AK 8 TYR cc_start: 0.9147 (t80) cc_final: 0.8871 (t80) REVERT: AK 60 PHE cc_start: 0.8874 (t80) cc_final: 0.8471 (t80) REVERT: AK 117 MET cc_start: 0.7353 (mmt) cc_final: 0.6992 (mmp) REVERT: AK 130 GLU cc_start: 0.7703 (tt0) cc_final: 0.7104 (tt0) REVERT: B5 45 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.8950 (t) REVERT: B5 93 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8765 (mt) REVERT: B5 114 MET cc_start: 0.8939 (ttm) cc_final: 0.8640 (ttm) REVERT: AB 52 MET cc_start: 0.7813 (tpt) cc_final: 0.7368 (tpt) REVERT: AB 64 ASP cc_start: 0.7967 (m-30) cc_final: 0.7564 (t70) REVERT: AB 83 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8072 (ttmm) REVERT: A8 34 GLN cc_start: 0.7703 (tp-100) cc_final: 0.7486 (tp-100) REVERT: A8 95 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8272 (mt) REVERT: BJ 16 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8166 (p) REVERT: BJ 48 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8519 (tpt170) REVERT: BJ 84 MET cc_start: 0.7783 (mtt) cc_final: 0.7342 (mtt) REVERT: AJ 18 MET cc_start: 0.8056 (mmm) cc_final: 0.7784 (mmm) REVERT: AJ 315 LYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6281 (ttmm) REVERT: S5 23 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7080 (mm-30) REVERT: S5 76 ASN cc_start: 0.8732 (t0) cc_final: 0.8500 (t0) REVERT: S5 91 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6378 (p90) REVERT: A3 45 ASN cc_start: 0.9044 (t0) cc_final: 0.8598 (t0) REVERT: A3 59 ASP cc_start: 0.4171 (p0) cc_final: 0.3559 (t0) REVERT: B3 29 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7540 (mt-10) REVERT: C2 11 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6844 (pp) REVERT: C2 80 ASP cc_start: 0.8311 (t0) cc_final: 0.8072 (t0) REVERT: C2 109 TYR cc_start: 0.8886 (m-80) cc_final: 0.8127 (m-80) REVERT: B4 27 GLU cc_start: 0.7876 (pp20) cc_final: 0.7534 (tm-30) REVERT: B4 40 SER cc_start: 0.9541 (p) cc_final: 0.9199 (t) REVERT: B4 43 LYS cc_start: 0.9138 (mtpm) cc_final: 0.8808 (ttmm) REVERT: B4 47 GLN cc_start: 0.8480 (mt0) cc_final: 0.8192 (mt0) REVERT: B4 74 ASN cc_start: 0.7727 (t0) cc_final: 0.7398 (t0) REVERT: AM 49 MET cc_start: 0.7203 (tmm) cc_final: 0.6714 (tmm) REVERT: AM 85 MET cc_start: 0.8082 (mmt) cc_final: 0.7715 (mmt) REVERT: B6 14 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8994 (tp) REVERT: B6 31 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5421 (pp20) REVERT: B7 44 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7325 (mm-30) REVERT: B7 49 GLN cc_start: 0.8289 (tp-100) cc_final: 0.7465 (tp-100) REVERT: B7 102 GLU cc_start: 0.8591 (tp30) cc_final: 0.8314 (tp30) REVERT: B9 67 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8200 (mm-30) REVERT: B9 96 TYR cc_start: 0.8288 (m-80) cc_final: 0.7949 (m-80) REVERT: B9 134 ARG cc_start: 0.8178 (tmt170) cc_final: 0.7634 (tmm160) REVERT: B2 26 GLU cc_start: 0.8628 (tp30) cc_final: 0.8292 (tp30) REVERT: B8 58 ARG cc_start: 0.8263 (mpp80) cc_final: 0.7974 (mpp80) REVERT: B8 71 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8754 (mp) REVERT: B8 90 ASP cc_start: 0.6973 (p0) cc_final: 0.6568 (p0) REVERT: B8 103 LYS cc_start: 0.8086 (mttt) cc_final: 0.7769 (tttp) REVERT: B8 122 TYR cc_start: 0.8233 (m-10) cc_final: 0.7779 (m-10) REVERT: BK 68 ILE cc_start: 0.8710 (tp) cc_final: 0.8346 (mm) REVERT: BK 83 TYR cc_start: 0.7518 (t80) cc_final: 0.7197 (t80) REVERT: C1 5 GLN cc_start: 0.7560 (pp30) cc_final: 0.6942 (pp30) REVERT: B1 8 ARG cc_start: 0.5863 (mmp-170) cc_final: 0.4703 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8380 (mm) REVERT: A1 28 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7538 (ttp80) REVERT: A1 34 ARG cc_start: 0.8564 (mmt90) cc_final: 0.7948 (mmt90) outliers start: 201 outliers final: 155 residues processed: 1226 average time/residue: 0.4807 time to fit residues: 988.6048 Evaluate side-chains 1259 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1083 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 75 LEU Chi-restraints excluded: chain D3 residue 81 THR Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 165 LEU Chi-restraints excluded: chain D1 residue 183 MET Chi-restraints excluded: chain D1 residue 239 THR Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 76 THR Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 122 MET Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain D6 residue 151 THR Chi-restraints excluded: chain 4L residue 39 SER Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 75 LEU Chi-restraints excluded: chain 4L residue 76 SER Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain 4L residue 94 ASN Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 61 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 150 MET Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 163 ASP Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 196 TRP Chi-restraints excluded: chain D5 residue 217 ILE Chi-restraints excluded: chain D5 residue 237 MET Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 251 THR Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 381 THR Chi-restraints excluded: chain D5 residue 383 MET Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 590 SER Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 9 MET Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 62 SER Chi-restraints excluded: chain D4 residue 78 MET Chi-restraints excluded: chain D4 residue 97 SER Chi-restraints excluded: chain D4 residue 106 LEU Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 195 MET Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 351 LEU Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 406 TYR Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 69 LEU Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 117 GLU Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 145 ILE Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 202 LEU Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 320 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 45 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain B5 residue 110 VAL Chi-restraints excluded: chain AB residue 8 LEU Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 40 LEU Chi-restraints excluded: chain AB residue 48 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain AB residue 85 ASP Chi-restraints excluded: chain A8 residue 11 ASP Chi-restraints excluded: chain A8 residue 15 GLN Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 35 CYS Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 48 ARG Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 60 TYR Chi-restraints excluded: chain BJ residue 83 CYS Chi-restraints excluded: chain BJ residue 98 ASP Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 279 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 14 ASP Chi-restraints excluded: chain S5 residue 49 ILE Chi-restraints excluded: chain S5 residue 54 GLU Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 43 LEU Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain B4 residue 8 SER Chi-restraints excluded: chain B4 residue 25 SER Chi-restraints excluded: chain B4 residue 64 LEU Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 124 PHE Chi-restraints excluded: chain AM residue 89 ASN Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 9 LEU Chi-restraints excluded: chain B9 residue 42 LEU Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B2 residue 7 ILE Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 71 LEU Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 264 optimal weight: 1.9990 chunk 425 optimal weight: 0.9980 chunk 259 optimal weight: 0.0010 chunk 201 optimal weight: 0.8980 chunk 295 optimal weight: 0.9990 chunk 446 optimal weight: 0.9990 chunk 410 optimal weight: 0.9980 chunk 355 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 103 GLN ** D4 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 374 ASN ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 116 GLN ** B4 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 89 ASN ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 77 GLN ** B2 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39024 Z= 0.233 Angle : 0.848 15.988 52894 Z= 0.406 Chirality : 0.045 0.220 5820 Planarity : 0.005 0.064 6543 Dihedral : 9.274 133.448 5502 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.80 % Favored : 90.18 % Rotamer: Outliers : 4.45 % Allowed : 27.31 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4561 helix: 1.32 (0.10), residues: 2776 sheet: -1.77 (1.09), residues: 20 loop : -3.04 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRPD2 167 HIS 0.013 0.001 HISD5 328 PHE 0.032 0.002 PHEB6 69 TYR 0.045 0.001 TYRB9 90 ARG 0.011 0.000 ARGD5 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9122 Ramachandran restraints generated. 4561 Oldfield, 0 Emsley, 4561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1114 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S2 29 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8231 (tmtt) REVERT: S2 34 ASN cc_start: 0.8528 (p0) cc_final: 0.8038 (p0) REVERT: D1 25 ARG cc_start: 0.8934 (ttm110) cc_final: 0.8329 (ttm-80) REVERT: D1 100 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8014 (pt) REVERT: D1 170 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7529 (mm-30) REVERT: D1 192 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7504 (tm-30) REVERT: D1 233 MET cc_start: 0.8538 (tmm) cc_final: 0.7712 (tmm) REVERT: D1 234 MET cc_start: 0.9019 (mmt) cc_final: 0.8590 (mpp) REVERT: D1 240 THR cc_start: 0.9207 (t) cc_final: 0.8848 (t) REVERT: D1 251 MET cc_start: 0.7947 (ttp) cc_final: 0.7508 (ptm) REVERT: D1 266 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8575 (tt) REVERT: D1 272 TRP cc_start: 0.6930 (t60) cc_final: 0.6143 (t-100) REVERT: D1 284 GLN cc_start: 0.7012 (mt0) cc_final: 0.6668 (pt0) REVERT: D1 317 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8019 (tm-30) REVERT: D6 2 MET cc_start: 0.5378 (tpp) cc_final: 0.5115 (mmt) REVERT: D6 98 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8624 (tm) REVERT: D6 114 GLU cc_start: 0.7766 (tt0) cc_final: 0.7336 (pm20) REVERT: D6 136 PHE cc_start: 0.8582 (p90) cc_final: 0.8199 (p90) REVERT: D6 148 SER cc_start: 0.7531 (p) cc_final: 0.7307 (t) REVERT: 4L 17 THR cc_start: 0.8935 (m) cc_final: 0.8727 (p) REVERT: 4L 34 GLU cc_start: 0.8668 (mm-30) cc_final: 0.7771 (tp30) REVERT: 4L 36 MET cc_start: 0.8305 (mtm) cc_final: 0.7296 (mtp) REVERT: D5 7 LEU cc_start: 0.8752 (mm) cc_final: 0.8403 (mt) REVERT: D5 86 SER cc_start: 0.8878 (m) cc_final: 0.8401 (t) REVERT: D5 87 MET cc_start: 0.7856 (tpp) cc_final: 0.7434 (tpp) REVERT: D5 150 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8467 (mmp) REVERT: D5 154 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8884 (mm) REVERT: D5 393 ASP cc_start: 0.8236 (m-30) cc_final: 0.7981 (m-30) REVERT: D5 397 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7945 (mt-10) REVERT: D5 487 LYS cc_start: 0.7545 (ttmp) cc_final: 0.7166 (ttmt) REVERT: D5 573 MET cc_start: 0.7628 (mtp) cc_final: 0.7359 (mtp) REVERT: D4 9 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6651 (tmm) REVERT: D4 17 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9040 (pp) REVERT: D4 25 ILE cc_start: 0.8516 (mm) cc_final: 0.8285 (mm) REVERT: D4 44 GLN cc_start: 0.8005 (pt0) cc_final: 0.7634 (pt0) REVERT: D4 105 PHE cc_start: 0.8241 (m-10) cc_final: 0.7969 (m-10) REVERT: D4 119 TYR cc_start: 0.8954 (t80) cc_final: 0.8533 (t80) REVERT: D4 121 MET cc_start: 0.8017 (mmm) cc_final: 0.7513 (tpp) REVERT: D4 123 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7377 (mt-10) REVERT: D4 141 GLU cc_start: 0.8407 (pm20) cc_final: 0.7596 (pp20) REVERT: D4 171 MET cc_start: 0.8511 (tmm) cc_final: 0.8222 (ttp) REVERT: D4 204 MET cc_start: 0.8662 (mmt) cc_final: 0.8303 (mpp) REVERT: D4 241 TYR cc_start: 0.8648 (t80) cc_final: 0.8368 (t80) REVERT: D4 257 MET cc_start: 0.6974 (mmm) cc_final: 0.6674 (mmm) REVERT: D4 263 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7713 (mmt) REVERT: D4 294 MET cc_start: 0.8824 (mmm) cc_final: 0.8472 (mmm) REVERT: D4 378 GLU cc_start: 0.7512 (tt0) cc_final: 0.6823 (tt0) REVERT: D4 400 MET cc_start: 0.7555 (tpp) cc_final: 0.7069 (tpp) REVERT: D2 14 MET cc_start: 0.7685 (tmm) cc_final: 0.7088 (tmm) REVERT: D2 79 MET cc_start: 0.8379 (mmm) cc_final: 0.7443 (mmm) REVERT: D2 91 ASN cc_start: 0.8545 (t0) cc_final: 0.8016 (t0) REVERT: D2 105 LYS cc_start: 0.8937 (tptp) cc_final: 0.8549 (mmmt) REVERT: D2 129 ILE cc_start: 0.8949 (tt) cc_final: 0.8617 (mt) REVERT: D2 130 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7720 (pp) REVERT: D2 139 MET cc_start: 0.7286 (mtt) cc_final: 0.6571 (mtp) REVERT: D2 171 ASN cc_start: 0.6713 (t0) cc_final: 0.6472 (t0) REVERT: D2 190 MET cc_start: 0.8320 (ttm) cc_final: 0.7915 (ttm) REVERT: D2 268 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8637 (tm-30) REVERT: AK 8 TYR cc_start: 0.9117 (t80) cc_final: 0.8770 (t80) REVERT: AK 60 PHE cc_start: 0.8925 (t80) cc_final: 0.8510 (t80) REVERT: AK 117 MET cc_start: 0.7424 (mmt) cc_final: 0.6936 (mpp) REVERT: AK 130 GLU cc_start: 0.7656 (tt0) cc_final: 0.7070 (tt0) REVERT: B5 93 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8808 (mt) REVERT: B5 114 MET cc_start: 0.8925 (ttm) cc_final: 0.8643 (ttm) REVERT: AB 52 MET cc_start: 0.7813 (tpt) cc_final: 0.7417 (tpt) REVERT: AB 64 ASP cc_start: 0.7875 (m-30) cc_final: 0.7585 (t70) REVERT: AB 83 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8143 (ttmm) REVERT: A8 34 GLN cc_start: 0.7703 (tp-100) cc_final: 0.7498 (tp-100) REVERT: A8 95 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8342 (mt) REVERT: BJ 16 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8145 (p) REVERT: BJ 84 MET cc_start: 0.7823 (mtt) cc_final: 0.7365 (mtt) REVERT: AJ 18 MET cc_start: 0.7973 (mmm) cc_final: 0.7701 (mmm) REVERT: AJ 315 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6372 (ttmm) REVERT: S5 23 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7149 (mm-30) REVERT: S5 60 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7602 (mt-10) REVERT: S5 76 ASN cc_start: 0.8698 (t0) cc_final: 0.8453 (t0) REVERT: S5 91 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6372 (p90) REVERT: A3 45 ASN cc_start: 0.9043 (t0) cc_final: 0.8626 (t0) REVERT: A3 59 ASP cc_start: 0.4068 (p0) cc_final: 0.3620 (t0) REVERT: B3 29 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C2 2 MET cc_start: 0.6097 (tmm) cc_final: 0.5561 (tmm) REVERT: C2 11 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6889 (pp) REVERT: C2 80 ASP cc_start: 0.8344 (t0) cc_final: 0.8139 (t0) REVERT: C2 82 MET cc_start: 0.8817 (tpt) cc_final: 0.8278 (tpt) REVERT: C2 109 TYR cc_start: 0.8912 (m-80) cc_final: 0.8139 (m-80) REVERT: B4 27 GLU cc_start: 0.7907 (pp20) cc_final: 0.7553 (tm-30) REVERT: B4 34 GLU cc_start: 0.7308 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B4 40 SER cc_start: 0.9555 (p) cc_final: 0.9208 (t) REVERT: B4 43 LYS cc_start: 0.9149 (mtpm) cc_final: 0.8838 (ttmm) REVERT: B4 45 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8251 (tp30) REVERT: B4 47 GLN cc_start: 0.8444 (mt0) cc_final: 0.8130 (mt0) REVERT: B4 74 ASN cc_start: 0.7736 (t0) cc_final: 0.7440 (t0) REVERT: B4 128 TYR cc_start: 0.7925 (p90) cc_final: 0.7659 (p90) REVERT: AM 49 MET cc_start: 0.7380 (tmm) cc_final: 0.7114 (tmm) REVERT: AM 50 MET cc_start: 0.8393 (tmt) cc_final: 0.8090 (tmm) REVERT: AM 85 MET cc_start: 0.8110 (mmt) cc_final: 0.7672 (mmt) REVERT: B6 14 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8993 (tp) REVERT: B6 31 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.5582 (pp20) REVERT: B7 17 GLU cc_start: 0.7656 (pm20) cc_final: 0.7351 (pm20) REVERT: B7 44 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7301 (mm-30) REVERT: B7 49 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7097 (tp-100) REVERT: B7 102 GLU cc_start: 0.8598 (tp30) cc_final: 0.8329 (tp30) REVERT: B9 18 LEU cc_start: 0.8811 (tt) cc_final: 0.8369 (tt) REVERT: B9 30 CYS cc_start: 0.6974 (t) cc_final: 0.6321 (t) REVERT: B9 67 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8119 (mm-30) REVERT: B9 96 TYR cc_start: 0.8304 (m-80) cc_final: 0.7924 (m-80) REVERT: B9 134 ARG cc_start: 0.8125 (tmt170) cc_final: 0.7568 (tmm160) REVERT: B2 26 GLU cc_start: 0.8618 (tp30) cc_final: 0.8299 (tp30) REVERT: B8 58 ARG cc_start: 0.8151 (mpp80) cc_final: 0.7938 (mpp80) REVERT: B8 83 MET cc_start: 0.8834 (tmm) cc_final: 0.8404 (tmm) REVERT: B8 90 ASP cc_start: 0.7014 (p0) cc_final: 0.6632 (p0) REVERT: B8 103 LYS cc_start: 0.8074 (mttt) cc_final: 0.7773 (tttp) REVERT: B8 122 TYR cc_start: 0.8300 (m-10) cc_final: 0.7839 (m-10) REVERT: BK 39 GLU cc_start: 0.8489 (mp0) cc_final: 0.8165 (mp0) REVERT: BK 50 ASP cc_start: 0.8024 (m-30) cc_final: 0.7487 (t70) REVERT: BK 54 ASP cc_start: 0.7915 (m-30) cc_final: 0.7630 (m-30) REVERT: BK 68 ILE cc_start: 0.8736 (tp) cc_final: 0.8413 (mm) REVERT: BK 83 TYR cc_start: 0.7518 (t80) cc_final: 0.7200 (t80) REVERT: C1 5 GLN cc_start: 0.7563 (pp30) cc_final: 0.6941 (pp30) REVERT: B1 8 ARG cc_start: 0.5862 (mmp-170) cc_final: 0.4696 (ptp-170) REVERT: A1 16 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8401 (mm) REVERT: A1 28 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7513 (ttp80) REVERT: A1 34 ARG cc_start: 0.8511 (mmt90) cc_final: 0.7919 (mmt90) outliers start: 182 outliers final: 151 residues processed: 1201 average time/residue: 0.4651 time to fit residues: 933.7466 Evaluate side-chains 1251 residues out of total 4093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1082 time to evaluate : 4.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 27 HIS Chi-restraints excluded: chain D3 residue 1 MET Chi-restraints excluded: chain D3 residue 75 LEU Chi-restraints excluded: chain D3 residue 81 THR Chi-restraints excluded: chain D1 residue 8 THR Chi-restraints excluded: chain D1 residue 22 LEU Chi-restraints excluded: chain D1 residue 100 LEU Chi-restraints excluded: chain D1 residue 136 VAL Chi-restraints excluded: chain D1 residue 165 LEU Chi-restraints excluded: chain D1 residue 183 MET Chi-restraints excluded: chain D1 residue 239 THR Chi-restraints excluded: chain D1 residue 266 LEU Chi-restraints excluded: chain D1 residue 287 HIS Chi-restraints excluded: chain D1 residue 289 LEU Chi-restraints excluded: chain D6 residue 20 PHE Chi-restraints excluded: chain D6 residue 41 CYS Chi-restraints excluded: chain D6 residue 56 VAL Chi-restraints excluded: chain D6 residue 98 LEU Chi-restraints excluded: chain D6 residue 106 TYR Chi-restraints excluded: chain D6 residue 122 MET Chi-restraints excluded: chain D6 residue 125 TRP Chi-restraints excluded: chain D6 residue 132 ASP Chi-restraints excluded: chain D6 residue 151 THR Chi-restraints excluded: chain 4L residue 43 LEU Chi-restraints excluded: chain 4L residue 79 VAL Chi-restraints excluded: chain 4L residue 94 ASN Chi-restraints excluded: chain D5 residue 9 LEU Chi-restraints excluded: chain D5 residue 61 MET Chi-restraints excluded: chain D5 residue 62 ILE Chi-restraints excluded: chain D5 residue 125 LEU Chi-restraints excluded: chain D5 residue 130 ILE Chi-restraints excluded: chain D5 residue 137 LEU Chi-restraints excluded: chain D5 residue 142 ILE Chi-restraints excluded: chain D5 residue 150 MET Chi-restraints excluded: chain D5 residue 154 LEU Chi-restraints excluded: chain D5 residue 163 ASP Chi-restraints excluded: chain D5 residue 172 ILE Chi-restraints excluded: chain D5 residue 180 ILE Chi-restraints excluded: chain D5 residue 217 ILE Chi-restraints excluded: chain D5 residue 237 MET Chi-restraints excluded: chain D5 residue 246 LEU Chi-restraints excluded: chain D5 residue 251 THR Chi-restraints excluded: chain D5 residue 373 LEU Chi-restraints excluded: chain D5 residue 380 LEU Chi-restraints excluded: chain D5 residue 381 THR Chi-restraints excluded: chain D5 residue 383 MET Chi-restraints excluded: chain D5 residue 395 ILE Chi-restraints excluded: chain D5 residue 404 THR Chi-restraints excluded: chain D5 residue 441 ILE Chi-restraints excluded: chain D5 residue 458 LEU Chi-restraints excluded: chain D5 residue 500 LEU Chi-restraints excluded: chain D5 residue 602 LEU Chi-restraints excluded: chain D4 residue 6 ILE Chi-restraints excluded: chain D4 residue 9 MET Chi-restraints excluded: chain D4 residue 17 LEU Chi-restraints excluded: chain D4 residue 62 SER Chi-restraints excluded: chain D4 residue 78 MET Chi-restraints excluded: chain D4 residue 103 GLN Chi-restraints excluded: chain D4 residue 106 LEU Chi-restraints excluded: chain D4 residue 126 LEU Chi-restraints excluded: chain D4 residue 183 VAL Chi-restraints excluded: chain D4 residue 195 MET Chi-restraints excluded: chain D4 residue 215 TRP Chi-restraints excluded: chain D4 residue 249 LEU Chi-restraints excluded: chain D4 residue 250 LEU Chi-restraints excluded: chain D4 residue 263 MET Chi-restraints excluded: chain D4 residue 269 MET Chi-restraints excluded: chain D4 residue 351 LEU Chi-restraints excluded: chain D4 residue 364 LEU Chi-restraints excluded: chain D4 residue 406 TYR Chi-restraints excluded: chain D2 residue 13 VAL Chi-restraints excluded: chain D2 residue 87 MET Chi-restraints excluded: chain D2 residue 117 GLU Chi-restraints excluded: chain D2 residue 130 LEU Chi-restraints excluded: chain D2 residue 146 LEU Chi-restraints excluded: chain D2 residue 153 LEU Chi-restraints excluded: chain D2 residue 202 LEU Chi-restraints excluded: chain D2 residue 226 THR Chi-restraints excluded: chain D2 residue 241 THR Chi-restraints excluded: chain D2 residue 246 ILE Chi-restraints excluded: chain D2 residue 248 LEU Chi-restraints excluded: chain D2 residue 266 ILE Chi-restraints excluded: chain D2 residue 284 ILE Chi-restraints excluded: chain D2 residue 287 LEU Chi-restraints excluded: chain D2 residue 289 ASN Chi-restraints excluded: chain D2 residue 297 THR Chi-restraints excluded: chain D2 residue 320 THR Chi-restraints excluded: chain D2 residue 328 THR Chi-restraints excluded: chain D2 residue 333 SER Chi-restraints excluded: chain D2 residue 343 LEU Chi-restraints excluded: chain AK residue 4 LEU Chi-restraints excluded: chain AK residue 55 THR Chi-restraints excluded: chain B5 residue 36 VAL Chi-restraints excluded: chain B5 residue 45 VAL Chi-restraints excluded: chain B5 residue 93 ILE Chi-restraints excluded: chain B5 residue 110 VAL Chi-restraints excluded: chain AB residue 32 VAL Chi-restraints excluded: chain AB residue 40 LEU Chi-restraints excluded: chain AB residue 48 VAL Chi-restraints excluded: chain AB residue 51 ILE Chi-restraints excluded: chain AB residue 85 ASP Chi-restraints excluded: chain A8 residue 11 ASP Chi-restraints excluded: chain A8 residue 15 GLN Chi-restraints excluded: chain A8 residue 17 VAL Chi-restraints excluded: chain A8 residue 35 CYS Chi-restraints excluded: chain A8 residue 36 ASP Chi-restraints excluded: chain A8 residue 95 LEU Chi-restraints excluded: chain A8 residue 109 CYS Chi-restraints excluded: chain A8 residue 120 ASP Chi-restraints excluded: chain A8 residue 168 PHE Chi-restraints excluded: chain BJ residue 16 THR Chi-restraints excluded: chain BJ residue 23 THR Chi-restraints excluded: chain BJ residue 51 ILE Chi-restraints excluded: chain BJ residue 60 TYR Chi-restraints excluded: chain BJ residue 81 VAL Chi-restraints excluded: chain BJ residue 83 CYS Chi-restraints excluded: chain BJ residue 98 ASP Chi-restraints excluded: chain BJ residue 145 LEU Chi-restraints excluded: chain BJ residue 163 LEU Chi-restraints excluded: chain AJ residue 76 ASN Chi-restraints excluded: chain AJ residue 132 PHE Chi-restraints excluded: chain AJ residue 160 VAL Chi-restraints excluded: chain AJ residue 174 VAL Chi-restraints excluded: chain AJ residue 259 LEU Chi-restraints excluded: chain AJ residue 311 ASP Chi-restraints excluded: chain AJ residue 315 LYS Chi-restraints excluded: chain S5 residue 14 ASP Chi-restraints excluded: chain S5 residue 49 ILE Chi-restraints excluded: chain S5 residue 54 GLU Chi-restraints excluded: chain S5 residue 91 TYR Chi-restraints excluded: chain S5 residue 92 THR Chi-restraints excluded: chain A3 residue 62 MET Chi-restraints excluded: chain B3 residue 31 VAL Chi-restraints excluded: chain B3 residue 60 VAL Chi-restraints excluded: chain C2 residue 11 LEU Chi-restraints excluded: chain C2 residue 26 LEU Chi-restraints excluded: chain C2 residue 43 LEU Chi-restraints excluded: chain C2 residue 68 PHE Chi-restraints excluded: chain B4 residue 8 SER Chi-restraints excluded: chain B4 residue 25 SER Chi-restraints excluded: chain B4 residue 72 SER Chi-restraints excluded: chain B4 residue 124 PHE Chi-restraints excluded: chain AM residue 71 MET Chi-restraints excluded: chain AM residue 89 ASN Chi-restraints excluded: chain AM residue 126 LEU Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 14 LEU Chi-restraints excluded: chain B6 residue 31 GLU Chi-restraints excluded: chain B6 residue 34 LEU Chi-restraints excluded: chain B6 residue 89 VAL Chi-restraints excluded: chain B7 residue 4 LEU Chi-restraints excluded: chain B7 residue 30 PHE Chi-restraints excluded: chain B9 residue 9 LEU Chi-restraints excluded: chain B9 residue 47 PHE Chi-restraints excluded: chain B9 residue 105 ASP Chi-restraints excluded: chain B9 residue 123 GLN Chi-restraints excluded: chain B2 residue 7 ILE Chi-restraints excluded: chain B2 residue 18 THR Chi-restraints excluded: chain B8 residue 9 LEU Chi-restraints excluded: chain B8 residue 13 TYR Chi-restraints excluded: chain B8 residue 16 THR Chi-restraints excluded: chain B8 residue 64 TRP Chi-restraints excluded: chain B8 residue 113 LEU Chi-restraints excluded: chain B8 residue 121 THR Chi-restraints excluded: chain B8 residue 138 LEU Chi-restraints excluded: chain B1 residue 16 VAL Chi-restraints excluded: chain B1 residue 48 LEU Chi-restraints excluded: chain A1 residue 16 LEU Chi-restraints excluded: chain A1 residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 282 optimal weight: 2.9990 chunk 378 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 327 optimal weight: 1.9990 chunk 52 optimal weight: 0.0070 chunk 98 optimal weight: 0.9980 chunk 355 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 103 GLN ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 77 GLN ** B2 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097035 restraints weight = 86655.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099585 restraints weight = 44324.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101369 restraints weight = 26967.947| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39024 Z= 0.232 Angle : 0.850 18.015 52894 Z= 0.405 Chirality : 0.045 0.259 5820 Planarity : 0.005 0.064 6543 Dihedral : 9.199 133.175 5502 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.76 % Favored : 90.22 % Rotamer: Outliers : 4.57 % Allowed : 27.66 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.35 % Twisted Proline : 0.72 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4561 helix: 1.33 (0.10), residues: 2781 sheet: -1.76 (1.11), residues: 20 loop : -3.02 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRPD1 118 HIS 0.011 0.001 HISA8 29 PHE 0.030 0.002 PHEB6 69 TYR 0.042 0.001 TYRB9 90 ARG 0.011 0.000 ARGBK 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14436.86 seconds wall clock time: 258 minutes 38.73 seconds (15518.73 seconds total)