Starting phenix.real_space_refine on Fri Feb 23 15:53:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbp_31884/02_2024/7vbp_31884_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbp_31884/02_2024/7vbp_31884.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbp_31884/02_2024/7vbp_31884_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbp_31884/02_2024/7vbp_31884_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbp_31884/02_2024/7vbp_31884_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbp_31884/02_2024/7vbp_31884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbp_31884/02_2024/7vbp_31884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbp_31884/02_2024/7vbp_31884_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbp_31884/02_2024/7vbp_31884_updated.pdb" } resolution = 2.8 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= 0.002 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 27 5.49 5 S 284 5.16 5 C 25352 2.51 5 N 6212 2.21 5 O 7147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q GLU 42": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 111": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 139": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "r GLU 378": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 248": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" 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: 39022 Number of models: 1 Model: "" Number of chains: 61 Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 333 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 949 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4761 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 939 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1022 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "w" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2586 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 114 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "l" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 245 Unusual residues: {'CDL': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "m" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "r" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 245 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "s" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {' UQ': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "j" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "k" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "l" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "m" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "s" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "w" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 20.63, per 1000 atoms: 0.53 Number of scatterers: 39022 At special positions: 0 Unit cell: (181.54, 190.133, 139.646, 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 284 16.00 P 27 15.00 O 7147 8.00 N 6212 7.00 C 25352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.06 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.04 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.02 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.94 Conformation dependent library (CDL) restraints added in 6.6 seconds 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 3 sheets defined 63.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.914A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 30 Proline residue: S 7 - end of helix removed outlier: 3.834A pdb=" N ILE S 18 " --> pdb=" O CYS S 15 " (cutoff:3.500A) Proline residue: S 19 - end of helix removed outlier: 4.040A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 33 through 99 Proline residue: W 73 - end of helix removed outlier: 3.666A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 124 No H-bonds generated for 'chain 'W' and resid 121 through 124' Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.279A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 95 through 97 No H-bonds generated for 'chain 'X' and resid 95 through 97' Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.626A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 4.073A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 53 removed outlier: 3.527A pdb=" N ALA Z 50 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG Z 52 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.854A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.583A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.870A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 175 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 3.773A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 through 132 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 72 Processing helix chain 'g' and resid 19 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 43 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.624A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.077A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.833A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.682A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 191 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.569A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.383A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 26 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.813A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 50 Processing helix chain 'k' and resid 55 through 85 Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.525A pdb=" N THR l 8 " --> pdb=" O PHE l 4 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU l 9 " --> pdb=" O ALA l 5 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.741A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 28 No H-bonds generated for 'chain 'l' and resid 26 through 28' Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.501A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 3.897A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 4.058A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.027A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.268A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.555A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.753A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.775A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 Processing helix chain 'l' and resid 448 through 471 removed outlier: 3.645A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 3.623A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 547 Proline residue: l 530 - end of helix removed outlier: 4.145A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix removed outlier: 4.215A pdb=" N SER l 543 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.891A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.349A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 34 removed outlier: 6.483A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.910A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.768A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 65 through 73 Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 4.074A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix removed outlier: 4.129A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 41 removed outlier: 4.210A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.765A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.530A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.585A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.501A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 142 through 171 removed outlier: 3.909A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.466A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 3.968A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 249 removed outlier: 3.501A pdb=" N LEU r 238 " --> pdb=" O LEU r 235 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY r 239 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR r 247 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR r 248 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 277 removed outlier: 4.694A pdb=" N TYR r 259 " --> pdb=" O ASN r 255 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 4.090A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.688A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.730A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.095A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.901A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.209A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 121 removed outlier: 4.392A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.919A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.600A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 4.857A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 11 through 13 No H-bonds generated for 'chain 'u' and resid 11 through 13' Processing helix chain 'u' and resid 22 through 35 removed outlier: 4.880A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 101 through 115 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 27 through 29 No H-bonds generated for 'chain 'v' and resid 27 through 29' Processing helix chain 'v' and resid 43 through 48 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.727A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 93 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.518A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 242 Processing helix chain 'w' and resid 246 through 250 Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 3.963A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.510A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'w' and resid 60 through 62 removed outlier: 6.813A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'w' and resid 84 through 86 2002 hydrogen bonds defined for protein. 5691 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: 12.88 Time building geometry restraints manager: 18.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 7160 1.33 - 1.48: 14755 1.48 - 1.63: 17203 1.63 - 1.78: 59 1.78 - 1.93: 496 Bond restraints: 39673 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C18 UQ s 402 " pdb=" C19 UQ s 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CA7 CDL a 201 " pdb=" OA8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL a 201 " pdb=" OB8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDL g 202 " pdb=" OA8 CDL g 202 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 ... (remaining 39668 not shown) Histogram of bond angle deviations from ideal: 80.46 - 91.30: 2 91.30 - 102.14: 227 102.14 - 112.98: 22533 112.98 - 123.82: 29684 123.82 - 134.67: 1169 Bond angle restraints: 53615 Sorted by residual: angle pdb=" N PRO Q 63 " pdb=" CD PRO Q 63 " pdb=" CG PRO Q 63 " ideal model delta sigma weight residual 103.20 83.39 19.81 1.50e+00 4.44e-01 1.74e+02 angle pdb=" CA PRO Q 63 " pdb=" CB PRO Q 63 " pdb=" CG PRO Q 63 " ideal model delta sigma weight residual 104.50 80.46 24.04 1.90e+00 2.77e-01 1.60e+02 angle pdb=" CA CYS V 95 " pdb=" CB CYS V 95 " pdb=" SG CYS V 95 " ideal model delta sigma weight residual 114.40 130.29 -15.89 2.30e+00 1.89e-01 4.77e+01 angle pdb=" C51 CDL r 504 " pdb=" CB5 CDL r 504 " pdb=" OB6 CDL r 504 " ideal model delta sigma weight residual 111.33 120.24 -8.91 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C11 CDL l 701 " pdb=" CA5 CDL l 701 " pdb=" OA6 CDL l 701 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.52e+01 ... (remaining 53610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 23229 34.83 - 69.66: 712 69.66 - 104.49: 62 104.49 - 139.32: 10 139.32 - 174.15: 13 Dihedral angle restraints: 24026 sinusoidal: 10388 harmonic: 13638 Sorted by residual: dihedral pdb=" CB CYS V 95 " pdb=" SG CYS V 95 " pdb=" SG CYS V 115 " pdb=" CB CYS V 115 " ideal model delta sinusoidal sigma weight residual -86.00 -17.54 -68.46 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS u 88 " pdb=" SG CYS u 88 " pdb=" SG CYS u 100 " pdb=" CB CYS u 100 " ideal model delta sinusoidal sigma weight residual 93.00 159.42 -66.42 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CA MET s 91 " pdb=" C MET s 91 " pdb=" N PRO s 92 " pdb=" CA PRO s 92 " ideal model delta harmonic sigma weight residual 0.00 -34.64 34.64 0 5.00e+00 4.00e-02 4.80e+01 ... (remaining 24023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4852 0.058 - 0.116: 881 0.116 - 0.174: 91 0.174 - 0.232: 8 0.232 - 0.291: 2 Chirality restraints: 5834 Sorted by residual: chirality pdb=" CA PHE i 90 " pdb=" N PHE i 90 " pdb=" C PHE i 90 " pdb=" CB PHE i 90 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA CYS V 95 " pdb=" N CYS V 95 " pdb=" C CYS V 95 " pdb=" CB CYS V 95 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA TRP u 48 " pdb=" N TRP u 48 " pdb=" C TRP u 48 " pdb=" CB TRP u 48 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5831 not shown) Planarity restraints: 6564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.424 2.00e-02 2.50e+03 4.60e-01 2.64e+03 pdb=" C11 UQ s 402 " -0.087 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.543 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.631 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " 0.422 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " 0.187 2.00e-02 2.50e+03 2.19e-01 6.01e+02 pdb=" C13 UQ s 402 " -0.123 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " -0.354 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " 0.037 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " 0.252 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " -0.119 2.00e-02 2.50e+03 1.86e-01 4.31e+02 pdb=" C18 UQ s 402 " 0.043 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " 0.337 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " -0.062 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " -0.198 2.00e-02 2.50e+03 ... (remaining 6561 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 162 2.37 - 3.00: 20917 3.00 - 3.64: 60179 3.64 - 4.27: 96015 4.27 - 4.90: 157237 Nonbonded interactions: 334510 Sorted by model distance: nonbonded pdb=" OE2 GLU l 397 " pdb=" O HOH l 801 " model vdw 1.741 2.440 nonbonded pdb=" O ILE w 66 " pdb=" O2A ADP w 401 " model vdw 1.807 3.040 nonbonded pdb=" OH TYR Q 53 " pdb=" O3 PEE Q 101 " model vdw 1.845 2.440 nonbonded pdb=" O HOH i 417 " pdb=" O HOH i 420 " model vdw 1.903 2.440 nonbonded pdb=" OE2 GLU a 95 " pdb=" O1 CDL a 201 " model vdw 1.903 2.440 ... (remaining 334505 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.510 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: 0.030 Extract box with map and model: 29.060 Check model and map are aligned: 0.650 Set scattering table: 0.430 Process input model: 102.920 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.160 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 0.264 39673 Z= 0.465 Angle : 0.885 24.042 53615 Z= 0.449 Chirality : 0.045 0.291 5834 Planarity : 0.009 0.460 6564 Dihedral : 16.736 174.151 15194 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Rotamer: Outliers : 0.32 % Allowed : 0.22 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % 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: 1.21 (0.12), residues: 4586 helix: 1.53 (0.09), residues: 2961 sheet: -1.17 (1.11), residues: 26 loop : -0.48 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP l 68 HIS 0.010 0.001 HIS l 56 PHE 0.037 0.002 PHE s 270 TYR 0.024 0.002 TYR b 88 ARG 0.007 0.001 ARG u 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 730 time to evaluate : 4.783 Fit side-chains REVERT: Q 63 PRO cc_start: 0.8021 (OUTLIER) cc_final: 0.7747 (Cg_exo) REVERT: l 397 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7515 (mt-10) REVERT: v 29 TYR cc_start: 0.7860 (t80) cc_final: 0.7556 (t80) REVERT: v 106 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7435 (ptm160) outliers start: 13 outliers final: 5 residues processed: 737 average time/residue: 1.8276 time to fit residues: 1584.5709 Evaluate side-chains 612 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 606 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 63 PRO Chi-restraints excluded: chain s residue 96 ILE Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 62 VAL Chi-restraints excluded: chain w residue 242 LYS Chi-restraints excluded: chain w residue 243 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 355 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 264 optimal weight: 0.6980 chunk 411 optimal weight: 0.0670 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 52 ASN Z 21 GLN Z 33 GLN b 83 HIS c 164 ASN d 54 GLN d 134 GLN e 145 ASN f 61 GLN i 49 ASN l 59 GLN l 205 ASN l 351 ASN l 405 ASN l 446 ASN ** p 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 26 ASN r 144 ASN r 304 GLN s 47 GLN u 73 GLN v 4 HIS v 65 GLN w 132 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39673 Z= 0.165 Angle : 0.556 11.087 53615 Z= 0.276 Chirality : 0.040 0.178 5834 Planarity : 0.005 0.077 6564 Dihedral : 15.138 143.056 6069 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 1.72 % Allowed : 7.92 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.58 (0.13), residues: 4586 helix: 1.88 (0.10), residues: 2949 sheet: -0.46 (1.17), residues: 25 loop : -0.47 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP l 68 HIS 0.007 0.001 HIS r 30 PHE 0.027 0.001 PHE i 292 TYR 0.026 0.001 TYR r 406 ARG 0.006 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 653 time to evaluate : 4.992 Fit side-chains REVERT: U 11 ASN cc_start: 0.8180 (t0) cc_final: 0.7847 (t0) REVERT: a 72 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7644 (ttm-80) REVERT: d 15 ARG cc_start: 0.7626 (ptm-80) cc_final: 0.7408 (ttm170) REVERT: d 60 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7875 (tpm170) REVERT: e 146 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8446 (ptmt) REVERT: i 48 PHE cc_start: 0.7244 (t80) cc_final: 0.7036 (t80) REVERT: j 16 LEU cc_start: 0.7944 (tt) cc_final: 0.7468 (tp) REVERT: l 320 ASN cc_start: 0.7836 (t0) cc_final: 0.7599 (t0) REVERT: l 493 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7617 (p) REVERT: l 496 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6436 (ttt) REVERT: m 57 PHE cc_start: 0.8150 (t80) cc_final: 0.7917 (t80) REVERT: n 46 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7717 (tmtt) REVERT: o 111 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8352 (mtmp) REVERT: o 118 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6687 (mt-10) REVERT: p 123 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: p 135 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7128 (ttm110) REVERT: r 103 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8739 (tt0) REVERT: u 17 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: v 29 TYR cc_start: 0.7811 (t80) cc_final: 0.7507 (t80) REVERT: w 63 ASP cc_start: 0.7565 (m-30) cc_final: 0.7200 (m-30) REVERT: w 95 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8715 (m-30) REVERT: w 241 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6438 (t80) outliers start: 70 outliers final: 19 residues processed: 681 average time/residue: 1.7883 time to fit residues: 1443.2037 Evaluate side-chains 640 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 608 time to evaluate : 4.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 111 LYS Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 342 optimal weight: 0.0670 chunk 280 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 412 optimal weight: 10.0000 chunk 445 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 408 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 330 optimal weight: 5.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN c 164 ASN c 183 HIS d 134 GLN e 145 ASN f 61 GLN g 14 GLN l 175 ASN l 351 ASN l 405 ASN r 168 GLN r 304 GLN u 64 ASN v 65 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 39673 Z= 0.383 Angle : 0.686 13.555 53615 Z= 0.342 Chirality : 0.047 0.215 5834 Planarity : 0.006 0.068 6564 Dihedral : 14.809 147.075 6054 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 2.41 % Allowed : 10.13 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.28 (0.12), residues: 4586 helix: 1.61 (0.09), residues: 2946 sheet: -0.59 (1.13), residues: 26 loop : -0.51 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP l 68 HIS 0.008 0.002 HIS r 30 PHE 0.029 0.002 PHE i 292 TYR 0.025 0.002 TYR X 155 ARG 0.009 0.001 ARG v 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 628 time to evaluate : 4.699 Fit side-chains revert: symmetry clash REVERT: a 72 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7708 (ttm-80) REVERT: b 93 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8370 (mmtm) REVERT: d 60 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7799 (tpm170) REVERT: e 146 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8526 (ptmt) REVERT: e 151 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: g 97 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8715 (tttm) REVERT: i 299 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8348 (m) REVERT: j 16 LEU cc_start: 0.8060 (tt) cc_final: 0.7582 (tp) REVERT: l 320 ASN cc_start: 0.7890 (t0) cc_final: 0.7690 (t0) REVERT: l 493 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.7918 (p) REVERT: l 496 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6578 (ttt) REVERT: m 57 PHE cc_start: 0.8332 (t80) cc_final: 0.8091 (t80) REVERT: p 123 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: r 103 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8822 (tt0) REVERT: s 258 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8165 (t0) REVERT: u 17 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: v 29 TYR cc_start: 0.7881 (t80) cc_final: 0.7669 (t80) REVERT: w 72 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6211 (ptm160) REVERT: w 95 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8778 (m-30) REVERT: w 220 LYS cc_start: 0.7138 (mtmt) cc_final: 0.6870 (tptp) REVERT: w 227 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6398 (mmm) REVERT: w 241 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7519 (t80) outliers start: 98 outliers final: 40 residues processed: 676 average time/residue: 1.7522 time to fit residues: 1401.4987 Evaluate side-chains 664 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 607 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 197 ASP Chi-restraints excluded: chain l residue 267 MET Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 371 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 276 optimal weight: 0.7980 chunk 413 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 216 optimal weight: 0.0670 chunk 391 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN c 164 ASN d 54 GLN d 134 GLN f 61 GLN g 63 GLN i 221 HIS i 319 HIS j 108 GLN l 446 ASN o 75 ASN r 366 ASN u 64 ASN v 65 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39673 Z= 0.228 Angle : 0.585 10.260 53615 Z= 0.294 Chirality : 0.042 0.231 5834 Planarity : 0.005 0.057 6564 Dihedral : 14.212 142.859 6054 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 2.58 % Allowed : 11.56 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.45 (0.13), residues: 4586 helix: 1.79 (0.10), residues: 2933 sheet: -0.50 (1.12), residues: 26 loop : -0.52 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 PHE 0.028 0.002 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.006 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 621 time to evaluate : 4.345 Fit side-chains revert: symmetry clash REVERT: X 81 ASP cc_start: 0.7935 (m-30) cc_final: 0.7553 (m-30) REVERT: a 72 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7678 (ttm-80) REVERT: e 69 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8299 (mtpt) REVERT: e 151 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: g 97 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8649 (tttm) REVERT: j 16 LEU cc_start: 0.8033 (tt) cc_final: 0.7593 (tp) REVERT: j 17 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8151 (mp) REVERT: k 1 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6126 (ttt) REVERT: l 493 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7836 (p) REVERT: l 496 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6448 (ttt) REVERT: m 57 PHE cc_start: 0.8280 (t80) cc_final: 0.8023 (t80) REVERT: n 46 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7813 (tmtt) REVERT: p 123 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: r 103 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8702 (tt0) REVERT: r 114 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: u 17 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: v 29 TYR cc_start: 0.7881 (t80) cc_final: 0.7664 (t80) REVERT: v 39 MET cc_start: 0.8259 (tpt) cc_final: 0.7925 (tpt) REVERT: w 72 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6232 (ptm160) REVERT: w 95 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8747 (m-30) REVERT: w 220 LYS cc_start: 0.7124 (mtmt) cc_final: 0.6862 (tptm) REVERT: w 227 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7265 (mmt) REVERT: w 241 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7835 (t80) outliers start: 105 outliers final: 44 residues processed: 667 average time/residue: 1.7937 time to fit residues: 1416.5073 Evaluate side-chains 669 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 608 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 304 MET Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 53 MET Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 197 ASP Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 495 ILE Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain p residue 13 GLN Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 373 optimal weight: 6.9990 chunk 302 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 393 optimal weight: 5.9990 chunk 110 optimal weight: 0.0770 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 54 GLN d 134 GLN f 61 GLN o 75 ASN r 399 ASN ** s 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN v 54 GLN v 110 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39673 Z= 0.197 Angle : 0.555 11.445 53615 Z= 0.278 Chirality : 0.040 0.196 5834 Planarity : 0.005 0.056 6564 Dihedral : 13.482 143.103 6054 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 2.68 % Allowed : 12.10 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.60 (0.13), residues: 4586 helix: 1.89 (0.10), residues: 2944 sheet: -0.30 (1.11), residues: 26 loop : -0.46 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 PHE 0.029 0.001 PHE i 292 TYR 0.020 0.001 TYR r 406 ARG 0.006 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 630 time to evaluate : 4.926 Fit side-chains revert: symmetry clash REVERT: U 11 ASN cc_start: 0.8168 (t0) cc_final: 0.7784 (t0) REVERT: X 81 ASP cc_start: 0.7932 (m-30) cc_final: 0.7557 (m-30) REVERT: b 93 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8272 (mmtm) REVERT: d 36 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8430 (mt) REVERT: d 60 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7746 (tpm170) REVERT: e 151 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: i 274 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: j 16 LEU cc_start: 0.8006 (tt) cc_final: 0.7585 (tp) REVERT: j 17 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8148 (mp) REVERT: k 37 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8132 (ttp) REVERT: l 140 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8936 (tt) REVERT: l 351 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8354 (m110) REVERT: l 493 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7792 (p) REVERT: l 496 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6442 (ttt) REVERT: m 57 PHE cc_start: 0.8190 (t80) cc_final: 0.7970 (t80) REVERT: n 46 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7801 (tmtt) REVERT: p 123 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: r 103 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: r 114 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: s 258 ASN cc_start: 0.8308 (m-40) cc_final: 0.8028 (t0) REVERT: u 17 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6891 (mm-30) REVERT: w 72 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.6203 (ptm160) REVERT: w 95 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8729 (m-30) REVERT: w 175 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7656 (mtt90) REVERT: w 220 LYS cc_start: 0.7116 (mtmt) cc_final: 0.6867 (tptm) REVERT: w 241 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8131 (t80) outliers start: 109 outliers final: 38 residues processed: 680 average time/residue: 1.7654 time to fit residues: 1421.6150 Evaluate side-chains 675 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 618 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 197 ASP Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 351 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 495 ILE Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 3.9990 chunk 394 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 257 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 438 optimal weight: 6.9990 chunk 363 optimal weight: 5.9990 chunk 202 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 33 GLN c 164 ASN d 54 GLN d 134 GLN f 61 GLN p 51 HIS r 51 ASN ** s 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN u 65 GLN v 54 GLN v 65 GLN ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 39673 Z= 0.255 Angle : 0.590 12.551 53615 Z= 0.296 Chirality : 0.042 0.189 5834 Planarity : 0.005 0.055 6564 Dihedral : 13.345 144.144 6054 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 2.58 % Allowed : 13.11 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.52 (0.13), residues: 4586 helix: 1.82 (0.10), residues: 2954 sheet: -0.29 (1.09), residues: 26 loop : -0.46 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 PHE 0.029 0.002 PHE i 292 TYR 0.019 0.002 TYR r 406 ARG 0.007 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 623 time to evaluate : 4.824 Fit side-chains revert: symmetry clash REVERT: U 11 ASN cc_start: 0.8171 (t0) cc_final: 0.7764 (t0) REVERT: V 138 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: X 81 ASP cc_start: 0.7955 (m-30) cc_final: 0.7580 (m-30) REVERT: b 93 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8284 (mmtm) REVERT: d 36 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8445 (mt) REVERT: d 60 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7693 (tpm170) REVERT: e 64 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6994 (tt0) REVERT: e 151 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: g 97 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8652 (tttm) REVERT: j 16 LEU cc_start: 0.8027 (tt) cc_final: 0.7608 (tp) REVERT: j 17 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8155 (mp) REVERT: l 140 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8965 (tt) REVERT: l 493 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7892 (p) REVERT: l 496 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6436 (ttt) REVERT: l 525 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.6880 (mpp) REVERT: m 57 PHE cc_start: 0.8212 (t80) cc_final: 0.7982 (t80) REVERT: n 46 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7818 (tmtt) REVERT: p 123 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: r 103 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8720 (tt0) REVERT: r 114 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: s 25 ARG cc_start: 0.8335 (mtp180) cc_final: 0.8122 (mtp180) REVERT: s 258 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8094 (t0) REVERT: u 17 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6960 (mm-30) REVERT: v 39 MET cc_start: 0.8286 (tpt) cc_final: 0.7921 (tpt) REVERT: w 72 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6214 (ptm160) REVERT: w 95 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8738 (m-30) REVERT: w 220 LYS cc_start: 0.7150 (mtmt) cc_final: 0.6915 (tptm) REVERT: w 227 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6330 (mmm) REVERT: w 241 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8184 (t80) outliers start: 105 outliers final: 49 residues processed: 665 average time/residue: 1.7994 time to fit residues: 1431.2878 Evaluate side-chains 682 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 611 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 197 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 249 optimal weight: 0.0570 chunk 320 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 368 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 436 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN c 164 ASN d 134 GLN e 148 GLN f 61 GLN ** s 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN v 110 GLN w 202 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 39673 Z= 0.243 Angle : 0.582 11.343 53615 Z= 0.293 Chirality : 0.042 0.186 5834 Planarity : 0.005 0.055 6564 Dihedral : 13.087 145.853 6054 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.03 % Rotamer: Outliers : 2.48 % Allowed : 13.65 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.53 (0.13), residues: 4586 helix: 1.82 (0.10), residues: 2954 sheet: -0.40 (1.06), residues: 26 loop : -0.46 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 PHE 0.029 0.002 PHE i 292 TYR 0.019 0.002 TYR r 406 ARG 0.005 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 621 time to evaluate : 5.068 Fit side-chains revert: symmetry clash REVERT: U 11 ASN cc_start: 0.8161 (t0) cc_final: 0.7773 (t0) REVERT: U 39 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8293 (m) REVERT: V 138 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: X 81 ASP cc_start: 0.7952 (m-30) cc_final: 0.7575 (m-30) REVERT: b 9 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8610 (mmtt) REVERT: b 93 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8259 (mmtm) REVERT: d 36 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8461 (mt) REVERT: d 60 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7719 (tpm170) REVERT: e 64 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: e 151 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: g 97 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8645 (tttm) REVERT: j 16 LEU cc_start: 0.8029 (tt) cc_final: 0.7626 (tp) REVERT: j 17 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8156 (mp) REVERT: k 37 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8181 (ttp) REVERT: l 140 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8956 (tt) REVERT: l 493 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.7895 (p) REVERT: l 496 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6380 (ttt) REVERT: l 525 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.6842 (mpp) REVERT: m 57 PHE cc_start: 0.8212 (t80) cc_final: 0.7980 (t80) REVERT: n 46 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7816 (tmtt) REVERT: p 123 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: r 103 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8703 (tt0) REVERT: r 114 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: s 258 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8093 (t0) REVERT: u 17 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6948 (mm-30) REVERT: v 39 MET cc_start: 0.8347 (tpt) cc_final: 0.7943 (tpt) REVERT: w 72 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.6220 (ptm160) REVERT: w 95 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8737 (m-30) REVERT: w 175 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7653 (mtt90) REVERT: w 220 LYS cc_start: 0.7156 (mtmt) cc_final: 0.6923 (tptm) REVERT: w 227 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6250 (mmm) REVERT: w 241 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7724 (t80) outliers start: 101 outliers final: 51 residues processed: 667 average time/residue: 1.7571 time to fit residues: 1388.4363 Evaluate side-chains 684 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 609 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 95 CYS Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Z residue 23 LYS Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain h residue 54 LYS Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 197 ASP Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 371 THR Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain s residue 72 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 260 optimal weight: 0.9990 chunk 131 optimal weight: 0.0020 chunk 85 optimal weight: 9.9990 chunk 84 optimal weight: 0.2980 chunk 277 optimal weight: 7.9990 chunk 297 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 343 optimal weight: 1.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 134 GLN d 149 HIS e 148 GLN f 61 GLN ** s 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN v 54 GLN v 110 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 39673 Z= 0.164 Angle : 0.529 11.312 53615 Z= 0.265 Chirality : 0.039 0.178 5834 Planarity : 0.005 0.056 6564 Dihedral : 12.500 145.234 6054 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 1.99 % Allowed : 14.49 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.72 (0.13), residues: 4586 helix: 1.99 (0.10), residues: 2955 sheet: -0.21 (1.06), residues: 26 loop : -0.42 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP l 144 HIS 0.007 0.001 HIS r 30 PHE 0.028 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.007 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 631 time to evaluate : 5.023 Fit side-chains revert: symmetry clash REVERT: U 11 ASN cc_start: 0.8148 (t0) cc_final: 0.7911 (t0) REVERT: V 138 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: X 81 ASP cc_start: 0.7940 (m-30) cc_final: 0.7573 (m-30) REVERT: d 36 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8457 (mt) REVERT: d 60 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7632 (tpm170) REVERT: g 97 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8568 (tttm) REVERT: i 274 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: i 324 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7561 (mptp) REVERT: j 16 LEU cc_start: 0.7996 (tt) cc_final: 0.7593 (tp) REVERT: j 17 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8118 (mp) REVERT: l 140 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8881 (tt) REVERT: l 493 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7787 (p) REVERT: l 496 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6329 (ttt) REVERT: m 57 PHE cc_start: 0.8118 (t80) cc_final: 0.7915 (t80) REVERT: n 46 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7784 (tmtt) REVERT: p 123 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: r 103 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8585 (tt0) REVERT: r 114 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: s 258 ASN cc_start: 0.8232 (m-40) cc_final: 0.7953 (t0) REVERT: u 17 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: v 39 MET cc_start: 0.8266 (tpt) cc_final: 0.7939 (tpt) REVERT: w 72 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6210 (ptm160) REVERT: w 220 LYS cc_start: 0.7148 (mtmt) cc_final: 0.6918 (tptm) REVERT: w 241 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7973 (t80) outliers start: 81 outliers final: 33 residues processed: 667 average time/residue: 1.7699 time to fit residues: 1399.9733 Evaluate side-chains 661 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 611 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain i residue 347 ASN Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 495 ILE Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 0.9980 chunk 418 optimal weight: 3.9990 chunk 381 optimal weight: 0.9980 chunk 406 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 367 optimal weight: 7.9990 chunk 384 optimal weight: 3.9990 chunk 405 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN c 164 ASN d 134 GLN e 148 GLN f 61 GLN ** s 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN u 65 GLN v 54 GLN v 110 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 39673 Z= 0.212 Angle : 0.565 14.497 53615 Z= 0.282 Chirality : 0.041 0.216 5834 Planarity : 0.005 0.055 6564 Dihedral : 12.468 145.067 6054 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 1.89 % Allowed : 14.76 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.70 (0.13), residues: 4586 helix: 1.95 (0.10), residues: 2957 sheet: -0.13 (1.06), residues: 26 loop : -0.40 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 PHE 0.029 0.001 PHE i 292 TYR 0.019 0.001 TYR l 422 ARG 0.007 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 613 time to evaluate : 5.111 Fit side-chains revert: symmetry clash REVERT: U 11 ASN cc_start: 0.8125 (t0) cc_final: 0.7898 (t0) REVERT: U 71 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7227 (mm-40) REVERT: V 138 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: X 81 ASP cc_start: 0.7955 (m-30) cc_final: 0.7588 (m-30) REVERT: d 36 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8460 (mt) REVERT: d 60 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7636 (tpm170) REVERT: e 64 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: g 97 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8589 (tttm) REVERT: i 274 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: i 324 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7564 (mptp) REVERT: j 16 LEU cc_start: 0.8033 (tt) cc_final: 0.7636 (tp) REVERT: j 17 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8124 (mp) REVERT: l 140 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8923 (tt) REVERT: l 493 VAL cc_start: 0.8202 (OUTLIER) cc_final: 0.7858 (p) REVERT: l 496 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6356 (ttt) REVERT: n 46 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7801 (tmtt) REVERT: p 123 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: r 103 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: r 114 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: s 258 ASN cc_start: 0.8291 (m-40) cc_final: 0.8009 (t0) REVERT: u 17 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6862 (mm-30) REVERT: w 72 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6209 (ptm160) REVERT: w 95 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8728 (m-30) REVERT: w 220 LYS cc_start: 0.7161 (mtmt) cc_final: 0.6926 (tptm) REVERT: w 241 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7999 (t80) outliers start: 77 outliers final: 38 residues processed: 652 average time/residue: 1.7738 time to fit residues: 1368.6609 Evaluate side-chains 668 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 610 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 89 ASN Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 498 PHE Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 0.9990 chunk 430 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 204 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 451 optimal weight: 0.7980 chunk 415 optimal weight: 2.9990 chunk 359 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 277 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN d 134 GLN e 148 GLN f 61 GLN i 49 ASN s 194 ASN ** s 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 ASN v 110 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 39673 Z= 0.168 Angle : 0.538 15.021 53615 Z= 0.268 Chirality : 0.039 0.272 5834 Planarity : 0.004 0.056 6564 Dihedral : 12.096 143.985 6054 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 1.84 % Allowed : 14.95 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.79 (0.13), residues: 4586 helix: 2.01 (0.10), residues: 2965 sheet: -0.01 (1.06), residues: 26 loop : -0.35 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP l 144 HIS 0.007 0.001 HIS r 30 PHE 0.028 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.007 0.000 ARG S 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 622 time to evaluate : 4.348 Fit side-chains revert: symmetry clash REVERT: U 11 ASN cc_start: 0.8129 (t0) cc_final: 0.7890 (t0) REVERT: U 71 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7281 (mm-40) REVERT: V 138 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: X 81 ASP cc_start: 0.7948 (m-30) cc_final: 0.7558 (m-30) REVERT: X 105 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7360 (mpp) REVERT: d 36 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8452 (mt) REVERT: d 60 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7622 (tpm170) REVERT: h 53 GLU cc_start: 0.7837 (tp30) cc_final: 0.7614 (tm-30) REVERT: i 274 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: i 324 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7577 (mptp) REVERT: j 16 LEU cc_start: 0.8005 (tt) cc_final: 0.7595 (tp) REVERT: j 17 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8094 (mp) REVERT: j 90 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8797 (mmm) REVERT: k 37 MET cc_start: 0.8377 (tmt) cc_final: 0.8154 (ttp) REVERT: l 140 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8867 (tt) REVERT: l 493 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7797 (p) REVERT: l 496 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6313 (ttt) REVERT: m 34 ILE cc_start: 0.7868 (mt) cc_final: 0.7530 (mt) REVERT: m 57 PHE cc_start: 0.8221 (t80) cc_final: 0.7916 (t80) REVERT: n 46 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7745 (tmtt) REVERT: p 123 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: r 103 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: r 114 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: s 258 ASN cc_start: 0.8222 (m-40) cc_final: 0.7950 (t0) REVERT: u 17 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: v 39 MET cc_start: 0.8097 (tpt) cc_final: 0.7819 (ttt) REVERT: w 72 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6187 (ptm160) REVERT: w 95 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8706 (m-30) REVERT: w 220 LYS cc_start: 0.7148 (mtmt) cc_final: 0.6919 (tptm) REVERT: w 227 MET cc_start: 0.7349 (mmm) cc_final: 0.7067 (mmm) REVERT: w 241 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8002 (t80) outliers start: 75 outliers final: 34 residues processed: 662 average time/residue: 1.7253 time to fit residues: 1353.1897 Evaluate side-chains 668 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 614 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain U residue 71 GLN Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 118 MET Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 274 GLU Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain l residue 25 ASN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 28 GLU Chi-restraints excluded: chain p residue 123 GLU Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 281 ASP Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 265 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 3.9990 chunk 382 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 359 optimal weight: 0.7980 chunk 150 optimal weight: 0.0870 chunk 369 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 74 GLN Z 33 GLN d 134 GLN e 145 ASN e 148 GLN f 61 GLN g 14 GLN r 399 ASN ** s 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 65 GLN v 54 GLN v 110 GLN w 306 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.133714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105434 restraints weight = 45706.519| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.24 r_work: 0.2936 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.100 39673 Z= 0.155 Angle : 0.528 14.582 53615 Z= 0.262 Chirality : 0.039 0.300 5834 Planarity : 0.004 0.057 6564 Dihedral : 11.716 141.937 6054 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 1.57 % Allowed : 15.45 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.88 (0.13), residues: 4586 helix: 2.09 (0.10), residues: 2965 sheet: 0.13 (1.05), residues: 26 loop : -0.33 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP l 144 HIS 0.006 0.001 HIS r 30 PHE 0.028 0.001 PHE i 292 TYR 0.023 0.001 TYR l 422 ARG 0.007 0.000 ARG S 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19664.80 seconds wall clock time: 349 minutes 14.91 seconds (20954.91 seconds total)