Starting phenix.real_space_refine on Fri Feb 23 20:20:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy9_32197/02_2024/7vy9_32197_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy9_32197/02_2024/7vy9_32197.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy9_32197/02_2024/7vy9_32197_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy9_32197/02_2024/7vy9_32197_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy9_32197/02_2024/7vy9_32197_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy9_32197/02_2024/7vy9_32197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy9_32197/02_2024/7vy9_32197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy9_32197/02_2024/7vy9_32197_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy9_32197/02_2024/7vy9_32197_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 36 5.49 5 S 294 5.16 5 C 26110 2.51 5 N 6289 2.21 5 O 6988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W GLU 131": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 25": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "a GLU 95": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 130": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 177": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "l TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 131": "OE1" <-> "OE2" Residue "p GLU 152": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 141": "OE1" <-> "OE2" Residue "s GLU 202": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "v GLU 116": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 238": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39717 Number of models: 1 Model: "" Number of chains: 42 Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 7, 'TRANS': 36} Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 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: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 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: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1295 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 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: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} 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: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1059 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 336 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "n" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 219 Unusual residues: {' UQ': 1, 'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.67 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.67 Time building chain proxies: 19.70, per 1000 atoms: 0.50 Number of scatterers: 39717 At special positions: 0 Unit cell: (182.614, 190.133, 138.572, 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 294 16.00 P 36 15.00 O 6988 8.00 N 6289 7.00 C 26110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " 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: 17.57 Conformation dependent library (CDL) restraints added in 6.7 seconds 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 202 helices and 3 sheets defined 63.2% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.11 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.966A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 31 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix removed outlier: 3.635A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 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 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 10 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 100 Proline residue: W 73 - end of helix removed outlier: 3.631A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASP W 100 " --> pdb=" O ILE W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 137 Processing helix chain 'W' and resid 139 through 142 No H-bonds generated for 'chain 'W' and resid 139 through 142' Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.842A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' 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: 3.788A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 54 removed outlier: 3.580A pdb=" N SER Z 54 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 removed outlier: 4.055A pdb=" N GLU Z 89 " --> pdb=" O GLU Z 85 " (cutoff:3.500A) 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: 3.793A 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 69 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 129 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.463A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.542A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) 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: 3.884A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.222A 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 174 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 Processing helix chain 'e' and resid 116 through 131 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 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.738A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' 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 44 Processing helix chain 'h' and resid 49 through 55 removed outlier: 4.027A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.658A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) 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: 4.308A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.858A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.782A 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: 3.773A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.601A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 252 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.458A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.612A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.763A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 50 Processing helix chain 'k' and resid 55 through 85 removed outlier: 4.056A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 95 through 97 No H-bonds generated for 'chain 'k' and resid 95 through 97' Processing helix chain 'l' and resid 3 through 22 removed outlier: 3.538A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.462A 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: 3.860A 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: 3.865A 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: 4.106A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.106A 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: 4.198A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.587A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) removed outlier: 4.594A 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: 4.049A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (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 380 Processing helix chain 'l' and resid 387 through 400 removed outlier: 4.037A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.686A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 5.955A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.385A 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: 3.701A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.378A 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 533 Proline residue: l 530 - end of helix removed outlier: 4.235A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 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 25 through 47 removed outlier: 3.780A pdb=" N PHE m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 138 through 148 removed outlier: 4.070A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER m 148 " --> pdb=" O ALA m 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 34 removed outlier: 6.254A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.822A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.802A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) 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: 4.392A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' 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 142 removed outlier: 4.734A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (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 17 Proline residue: r 7 - end of helix Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.158A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 Proline residue: r 74 - end of helix removed outlier: 4.396A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.653A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.404A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.320A 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: 3.602A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (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: 4.545A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 3.979A 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 237 through 250 removed outlier: 5.460A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 278 removed outlier: 4.986A pdb=" N ALA r 258 " --> pdb=" O ASN r 255 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR r 259 " --> pdb=" O TYR r 256 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 4.453A pdb=" N TRP r 267 " --> pdb=" O LEU r 264 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY r 268 " --> pdb=" O SER r 265 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR r 272 " --> pdb=" O MET r 269 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS r 276 " --> 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: 3.543A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (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 392 through 415 removed outlier: 3.618A pdb=" N TYR r 409 " --> pdb=" O LEU r 405 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix 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: 3.703A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.398A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 3.799A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 157 removed outlier: 5.095A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN s 157 " --> pdb=" O VAL s 153 " (cutoff:3.500A) Processing helix chain 's' and resid 162 through 168 removed outlier: 4.073A pdb=" N ILE s 166 " --> pdb=" O LEU s 162 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 Processing helix chain 's' and resid 293 through 311 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: 4.869A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.723A 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 80 through 91 Processing helix chain 'u' and resid 102 through 113 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 43 through 49 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 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.716A 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 163 through 175 removed outlier: 4.651A pdb=" N PHE w 167 " --> pdb=" O ILE w 163 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL w 168 " --> pdb=" O TYR w 164 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE w 169 " --> pdb=" O SER w 165 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.130A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.676A 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 243 Processing helix chain 'w' and resid 245 through 251 removed outlier: 4.017A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 264 removed outlier: 4.272A pdb=" N GLU w 264 " --> pdb=" O ALA w 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 260 through 264' Processing helix chain 'w' and resid 266 through 275 removed outlier: 3.575A pdb=" N TYR w 275 " --> pdb=" O GLU w 271 " (cutoff:3.500A) 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 309 removed outlier: 5.006A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' 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: 6.568A 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 64 removed outlier: 6.795A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.537A 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 2020 hydrogen bonds defined for protein. 5808 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: 12.36 Time building geometry restraints manager: 17.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5988 1.31 - 1.44: 10990 1.44 - 1.56: 22982 1.56 - 1.69: 235 1.69 - 1.82: 531 Bond restraints: 40726 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 404 " pdb=" C19 UQ s 404 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C13 UQ s 404 " pdb=" C14 UQ s 404 " ideal model delta sigma weight residual 1.335 1.547 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C23 UQ s 404 " pdb=" C24 UQ s 404 " ideal model delta sigma weight residual 1.335 1.544 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C8 UQ s 404 " pdb=" C9 UQ s 404 " ideal model delta sigma weight residual 1.334 1.540 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 40721 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.07: 1289 106.07 - 113.13: 22412 113.13 - 120.19: 14666 120.19 - 127.26: 15989 127.26 - 134.32: 580 Bond angle restraints: 54936 Sorted by residual: angle pdb=" N ILE l 26 " pdb=" CA ILE l 26 " pdb=" C ILE l 26 " ideal model delta sigma weight residual 113.71 106.88 6.83 9.50e-01 1.11e+00 5.16e+01 angle pdb=" C11 CDL V 201 " pdb=" CA5 CDL V 201 " pdb=" OA6 CDL V 201 " ideal model delta sigma weight residual 111.33 120.39 -9.06 1.32e+00 5.72e-01 4.69e+01 angle pdb=" C51 CDL V 202 " pdb=" CB5 CDL V 202 " pdb=" OB6 CDL V 202 " ideal model delta sigma weight residual 111.33 120.30 -8.97 1.32e+00 5.72e-01 4.60e+01 angle pdb=" C11 CDL s 402 " pdb=" CA5 CDL s 402 " pdb=" OA6 CDL s 402 " ideal model delta sigma weight residual 111.33 120.27 -8.94 1.32e+00 5.72e-01 4.57e+01 angle pdb=" C51 CDL s 402 " pdb=" CB5 CDL s 402 " pdb=" OB6 CDL s 402 " ideal model delta sigma weight residual 111.33 120.26 -8.93 1.32e+00 5.72e-01 4.56e+01 ... (remaining 54931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 23488 34.93 - 69.85: 1210 69.85 - 104.78: 82 104.78 - 139.71: 16 139.71 - 174.63: 5 Dihedral angle restraints: 24801 sinusoidal: 10941 harmonic: 13860 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.63 -174.63 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -132.57 46.57 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA TYR j 37 " pdb=" C TYR j 37 " pdb=" N GLU j 38 " pdb=" CA GLU j 38 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 24798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 5309 0.065 - 0.131: 585 0.131 - 0.196: 28 0.196 - 0.262: 6 0.262 - 0.327: 3 Chirality restraints: 5931 Sorted by residual: chirality pdb=" CA TYR m 60 " pdb=" N TYR m 60 " pdb=" C TYR m 60 " pdb=" CB TYR m 60 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA LYS s 291 " pdb=" N LYS s 291 " pdb=" C LYS s 291 " pdb=" CB LYS s 291 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA TRP s 290 " pdb=" N TRP s 290 " pdb=" C TRP s 290 " pdb=" CB TRP s 290 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 5928 not shown) Planarity restraints: 6684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 404 " 0.403 2.00e-02 2.50e+03 3.60e-01 1.62e+03 pdb=" C18 UQ s 404 " -0.409 2.00e-02 2.50e+03 pdb=" C19 UQ s 404 " -0.398 2.00e-02 2.50e+03 pdb=" C20 UQ s 404 " 0.003 2.00e-02 2.50e+03 pdb=" C21 UQ s 404 " 0.401 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 404 " -0.070 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C11 UQ s 404 " 0.071 2.00e-02 2.50e+03 pdb=" C7 UQ s 404 " -0.277 2.00e-02 2.50e+03 pdb=" C8 UQ s 404 " 0.519 2.00e-02 2.50e+03 pdb=" C9 UQ s 404 " -0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 404 " -0.122 2.00e-02 2.50e+03 1.84e-01 4.23e+02 pdb=" C13 UQ s 404 " 0.050 2.00e-02 2.50e+03 pdb=" C14 UQ s 404 " 0.330 2.00e-02 2.50e+03 pdb=" C15 UQ s 404 " -0.060 2.00e-02 2.50e+03 pdb=" C16 UQ s 404 " -0.198 2.00e-02 2.50e+03 ... (remaining 6681 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2935 2.74 - 3.28: 39159 3.28 - 3.82: 68714 3.82 - 4.36: 83532 4.36 - 4.90: 141678 Nonbonded interactions: 336018 Sorted by model distance: nonbonded pdb=" O LEU m 61 " pdb=" OH TYR s 114 " model vdw 2.198 2.440 nonbonded pdb=" OE1 GLU s 24 " pdb=" OH TYR s 228 " model vdw 2.200 2.440 nonbonded pdb=" O LEU j 73 " pdb=" OH TYR s 160 " model vdw 2.200 2.440 nonbonded pdb=" NH2 ARG W 81 " pdb=" OD1 ASN u 64 " model vdw 2.202 2.520 nonbonded pdb=" O LEU i 19 " pdb=" OG SER i 23 " model vdw 2.221 2.440 ... (remaining 336013 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=0.67 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: 1.450 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: 0.050 Extract box with map and model: 8.290 Check model and map are aligned: 0.540 Set scattering table: 0.360 Process input model: 97.530 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.140 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:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 0.226 40726 Z= 0.495 Angle : 0.832 17.181 54936 Z= 0.418 Chirality : 0.042 0.327 5931 Planarity : 0.008 0.360 6684 Dihedral : 19.116 174.631 15826 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 0.99 % Allowed : 15.01 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 (0.12), residues: 4666 helix: 2.13 (0.10), residues: 2936 sheet: -0.66 (0.96), residues: 35 loop : -0.47 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS S 27 PHE 0.028 0.001 PHE i 292 TYR 0.024 0.001 TYR i 208 ARG 0.011 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 690 time to evaluate : 4.876 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 123 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8518 (mt-10) REVERT: c 149 ILE cc_start: 0.8566 (pp) cc_final: 0.8348 (pt) REVERT: e 111 ASP cc_start: 0.7480 (t70) cc_final: 0.7109 (t70) REVERT: e 115 GLN cc_start: 0.7820 (pt0) cc_final: 0.7564 (pt0) REVERT: i 208 TYR cc_start: 0.9151 (t80) cc_final: 0.8758 (t80) REVERT: j 66 ASP cc_start: 0.8830 (t0) cc_final: 0.8626 (t0) REVERT: l 383 MET cc_start: 0.8962 (tpp) cc_final: 0.8724 (tpt) REVERT: m 64 MET cc_start: 0.9357 (mmp) cc_final: 0.9023 (mmp) REVERT: o 111 LYS cc_start: 0.8721 (mtpp) cc_final: 0.7988 (mttt) REVERT: r 398 MET cc_start: 0.8349 (mmm) cc_final: 0.7659 (ttm) REVERT: u 88 CYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6623 (t) REVERT: w 241 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7212 (t80) outliers start: 41 outliers final: 23 residues processed: 714 average time/residue: 1.6575 time to fit residues: 1418.1558 Evaluate side-chains 697 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 672 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 8 SER Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 386 optimal weight: 3.9990 chunk 347 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 358 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 415 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN h 45 HIS i 47 ASN i 171 ASN k 50 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 12 HIS p 13 GLN p 53 ASN r 304 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40726 Z= 0.170 Angle : 0.524 9.160 54936 Z= 0.259 Chirality : 0.039 0.182 5931 Planarity : 0.004 0.064 6684 Dihedral : 16.623 175.300 6601 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 2.50 % Allowed : 13.77 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.87 (0.13), residues: 4666 helix: 2.19 (0.10), residues: 2938 sheet: -0.26 (1.12), residues: 25 loop : -0.41 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS l 534 PHE 0.028 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.008 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 697 time to evaluate : 4.333 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: S 48 MET cc_start: 0.9165 (mtp) cc_final: 0.8826 (mtm) REVERT: X 123 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8533 (mt-10) REVERT: Z 49 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: c 149 ILE cc_start: 0.8642 (pp) cc_final: 0.8383 (pt) REVERT: h 13 ASP cc_start: 0.8338 (t0) cc_final: 0.7987 (t0) REVERT: h 102 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: j 4 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8309 (mmt) REVERT: j 66 ASP cc_start: 0.8830 (t0) cc_final: 0.8614 (t0) REVERT: l 383 MET cc_start: 0.8954 (tpp) cc_final: 0.8674 (tpt) REVERT: m 99 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7410 (ttm) REVERT: o 111 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8317 (ttpp) REVERT: r 398 MET cc_start: 0.8403 (mmm) cc_final: 0.7842 (ttm) REVERT: s 227 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8484 (tp30) REVERT: u 155 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7889 (pp20) REVERT: v 39 MET cc_start: 0.8307 (tpt) cc_final: 0.7955 (tpp) REVERT: w 241 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.7391 (t80) outliers start: 103 outliers final: 39 residues processed: 743 average time/residue: 1.6840 time to fit residues: 1499.6695 Evaluate side-chains 732 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 686 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 4 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 231 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 346 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 416 optimal weight: 0.0040 chunk 450 optimal weight: 9.9990 chunk 371 optimal weight: 0.8980 chunk 413 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 334 optimal weight: 5.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN h 70 GLN i 47 ASN i 171 ASN k 50 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN u 77 HIS v 54 GLN w 107 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40726 Z= 0.258 Angle : 0.568 8.868 54936 Z= 0.284 Chirality : 0.042 0.195 5931 Planarity : 0.005 0.061 6684 Dihedral : 15.688 156.683 6575 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 3.20 % Allowed : 13.94 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.64 (0.12), residues: 4666 helix: 1.97 (0.09), residues: 2948 sheet: -0.24 (1.14), residues: 25 loop : -0.46 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS S 27 PHE 0.028 0.002 PHE i 292 TYR 0.023 0.002 TYR r 406 ARG 0.010 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 688 time to evaluate : 4.472 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 48 MET cc_start: 0.9181 (mtp) cc_final: 0.8889 (mtm) REVERT: U 16 GLU cc_start: 0.8227 (mm-30) cc_final: 0.8001 (mm-30) REVERT: Z 49 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: b 93 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8120 (mttt) REVERT: b 119 LEU cc_start: 0.8654 (mm) cc_final: 0.8393 (mp) REVERT: f 61 GLN cc_start: 0.8860 (tp40) cc_final: 0.8508 (tp-100) REVERT: h 13 ASP cc_start: 0.8374 (t0) cc_final: 0.7999 (t0) REVERT: h 102 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: j 66 ASP cc_start: 0.8851 (t0) cc_final: 0.8591 (t0) REVERT: j 85 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8263 (mttt) REVERT: m 99 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7432 (ttm) REVERT: m 135 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8299 (t80) REVERT: n 41 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8834 (mttm) REVERT: n 54 GLU cc_start: 0.7563 (pm20) cc_final: 0.7230 (mp0) REVERT: r 103 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.9149 (tt0) REVERT: r 302 MET cc_start: 0.9213 (mmp) cc_final: 0.8936 (mmp) REVERT: s 227 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8433 (tp30) REVERT: s 296 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9113 (tt) REVERT: w 241 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.7157 (t80) REVERT: w 293 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7787 (ttp80) outliers start: 132 outliers final: 61 residues processed: 742 average time/residue: 1.7090 time to fit residues: 1516.0561 Evaluate side-chains 743 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 671 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 99 LYS Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 492 ILE Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 411 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 198 optimal weight: 0.7980 chunk 279 optimal weight: 8.9990 chunk 418 optimal weight: 2.9990 chunk 442 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 396 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN b 13 GLN e 115 GLN e 148 GLN h 70 GLN i 47 ASN i 171 ASN k 50 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 GLN u 77 HIS v 54 GLN v 117 GLN w 107 GLN w 235 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40726 Z= 0.210 Angle : 0.538 9.314 54936 Z= 0.269 Chirality : 0.040 0.189 5931 Planarity : 0.004 0.061 6684 Dihedral : 15.163 154.970 6573 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 3.52 % Allowed : 14.52 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.69 (0.12), residues: 4666 helix: 2.01 (0.09), residues: 2949 sheet: -0.28 (1.13), residues: 25 loop : -0.45 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS S 27 PHE 0.028 0.001 PHE i 292 TYR 0.023 0.001 TYR r 406 ARG 0.009 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 683 time to evaluate : 4.346 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8506 (mmt) cc_final: 0.8156 (mmt) REVERT: S 48 MET cc_start: 0.9170 (mtp) cc_final: 0.8862 (mtm) REVERT: V 8 LYS cc_start: 0.8327 (mttt) cc_final: 0.8040 (mtmm) REVERT: Y 99 ILE cc_start: 0.7377 (mt) cc_final: 0.6889 (tt) REVERT: Z 49 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: b 93 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8031 (mttt) REVERT: b 119 LEU cc_start: 0.8630 (mm) cc_final: 0.8360 (mp) REVERT: d 73 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8084 (p0) REVERT: f 61 GLN cc_start: 0.8838 (tp40) cc_final: 0.8514 (tp-100) REVERT: h 13 ASP cc_start: 0.8425 (t0) cc_final: 0.7991 (t0) REVERT: h 102 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: j 66 ASP cc_start: 0.8823 (t0) cc_final: 0.8620 (t0) REVERT: j 85 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8233 (mttt) REVERT: m 99 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7408 (ttm) REVERT: n 41 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8823 (mttm) REVERT: n 54 GLU cc_start: 0.7622 (pm20) cc_final: 0.7239 (mp0) REVERT: o 111 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8270 (ttpp) REVERT: r 103 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9104 (tt0) REVERT: s 227 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8430 (tp30) REVERT: s 296 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9121 (tt) REVERT: w 227 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6915 (mtt) REVERT: w 238 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: w 241 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.7426 (t80) REVERT: w 272 ASP cc_start: 0.8044 (m-30) cc_final: 0.7600 (m-30) REVERT: w 293 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7808 (ttp80) outliers start: 145 outliers final: 71 residues processed: 752 average time/residue: 1.6625 time to fit residues: 1499.8238 Evaluate side-chains 746 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 662 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 320 ASN Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 238 GLU Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 368 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 377 optimal weight: 0.9980 chunk 306 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 397 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN d 134 GLN e 115 GLN e 148 GLN h 70 GLN i 47 ASN i 171 ASN k 50 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 230 ASN u 77 HIS v 54 GLN w 107 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40726 Z= 0.236 Angle : 0.553 10.968 54936 Z= 0.276 Chirality : 0.041 0.195 5931 Planarity : 0.005 0.061 6684 Dihedral : 14.769 155.125 6573 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 3.68 % Allowed : 15.01 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.63 (0.12), residues: 4666 helix: 1.97 (0.09), residues: 2955 sheet: -0.55 (0.96), residues: 35 loop : -0.48 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS S 27 PHE 0.028 0.001 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.011 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 672 time to evaluate : 4.892 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8514 (mmt) cc_final: 0.8175 (mmt) REVERT: S 48 MET cc_start: 0.9181 (mtp) cc_final: 0.8879 (mtm) REVERT: V 8 LYS cc_start: 0.8354 (mttt) cc_final: 0.8073 (mtmm) REVERT: Z 49 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: a 103 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: a 114 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8909 (ptmm) REVERT: a 152 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8868 (ttmm) REVERT: b 93 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8063 (mttt) REVERT: b 119 LEU cc_start: 0.8688 (mm) cc_final: 0.8434 (mp) REVERT: d 73 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8066 (p0) REVERT: g 16 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8652 (mt) REVERT: h 5 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8348 (t70) REVERT: h 13 ASP cc_start: 0.8502 (t0) cc_final: 0.7988 (t0) REVERT: h 55 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: h 102 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7250 (pt0) REVERT: j 85 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8234 (mttt) REVERT: l 411 MET cc_start: 0.8956 (mmp) cc_final: 0.8628 (mmp) REVERT: m 99 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7397 (ttm) REVERT: m 135 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8264 (t80) REVERT: n 41 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8815 (mttm) REVERT: n 54 GLU cc_start: 0.7615 (pm20) cc_final: 0.7245 (mp0) REVERT: r 103 GLN cc_start: 0.9380 (OUTLIER) cc_final: 0.9135 (tt0) REVERT: r 302 MET cc_start: 0.9221 (mmp) cc_final: 0.8879 (mmp) REVERT: s 227 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8394 (tp30) REVERT: s 296 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9115 (tt) REVERT: u 155 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7631 (pp20) REVERT: v 105 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: v 118 ARG cc_start: 0.6667 (tmm-80) cc_final: 0.6293 (ttp80) REVERT: w 238 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: w 241 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.7304 (t80) REVERT: w 293 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7826 (ttp80) outliers start: 152 outliers final: 79 residues processed: 751 average time/residue: 1.7202 time to fit residues: 1574.3729 Evaluate side-chains 767 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 667 time to evaluate : 4.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 320 ASN Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 238 GLU Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 148 optimal weight: 0.8980 chunk 398 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 259 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 443 optimal weight: 0.9980 chunk 367 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN e 148 GLN f 61 GLN h 70 GLN i 47 ASN i 171 ASN k 50 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS v 54 GLN w 107 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 40726 Z= 0.163 Angle : 0.517 9.350 54936 Z= 0.257 Chirality : 0.039 0.179 5931 Planarity : 0.004 0.062 6684 Dihedral : 14.108 153.999 6573 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 3.03 % Allowed : 15.88 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.80 (0.13), residues: 4666 helix: 2.13 (0.10), residues: 2948 sheet: -0.42 (0.96), residues: 35 loop : -0.45 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.004 0.001 HIS r 30 PHE 0.029 0.001 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.010 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 700 time to evaluate : 4.420 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8549 (mmt) cc_final: 0.8203 (mmt) REVERT: S 48 MET cc_start: 0.9170 (mtp) cc_final: 0.8860 (mtm) REVERT: V 8 LYS cc_start: 0.8341 (mttt) cc_final: 0.8059 (mtmm) REVERT: X 123 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8697 (mt-10) REVERT: Y 99 ILE cc_start: 0.7346 (mt) cc_final: 0.6862 (tt) REVERT: Z 49 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7923 (mm-30) REVERT: a 103 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: a 114 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8894 (ptmm) REVERT: a 152 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8835 (ttmm) REVERT: b 93 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7996 (mttt) REVERT: b 119 LEU cc_start: 0.8587 (mm) cc_final: 0.8326 (mp) REVERT: c 149 ILE cc_start: 0.8606 (pp) cc_final: 0.8403 (pt) REVERT: d 73 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8035 (p0) REVERT: g 16 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8587 (mt) REVERT: h 13 ASP cc_start: 0.8501 (t0) cc_final: 0.8015 (t0) REVERT: h 55 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: h 102 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7250 (pt0) REVERT: i 263 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8534 (pttt) REVERT: j 85 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8180 (mttt) REVERT: l 383 MET cc_start: 0.9000 (tpp) cc_final: 0.8725 (tpt) REVERT: l 411 MET cc_start: 0.8930 (mmp) cc_final: 0.8607 (mmp) REVERT: l 518 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8504 (mt0) REVERT: m 99 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7396 (ttm) REVERT: n 41 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8816 (mttm) REVERT: n 54 GLU cc_start: 0.7651 (pm20) cc_final: 0.7325 (mp0) REVERT: o 61 GLU cc_start: 0.7618 (pt0) cc_final: 0.7414 (pt0) REVERT: o 111 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8337 (ttpp) REVERT: p 59 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7794 (ptmt) REVERT: s 206 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8426 (mp0) REVERT: s 227 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8425 (tp30) REVERT: u 155 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: w 272 ASP cc_start: 0.8056 (m-30) cc_final: 0.7659 (m-30) REVERT: w 293 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7812 (ttp80) outliers start: 125 outliers final: 63 residues processed: 764 average time/residue: 1.6520 time to fit residues: 1513.3175 Evaluate side-chains 758 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 678 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 518 GLN Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 427 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 247 optimal weight: 0.7980 chunk 441 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN b 13 GLN e 148 GLN h 70 GLN i 47 ASN i 171 ASN k 50 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 103 GLN r 255 ASN u 77 HIS v 54 GLN w 107 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40726 Z= 0.222 Angle : 0.548 9.607 54936 Z= 0.272 Chirality : 0.041 0.192 5931 Planarity : 0.004 0.061 6684 Dihedral : 13.956 154.548 6572 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 3.20 % Allowed : 16.10 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 (0.12), residues: 4666 helix: 2.03 (0.09), residues: 2954 sheet: -0.55 (0.96), residues: 35 loop : -0.46 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.005 0.001 HIS S 27 PHE 0.028 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.010 0.000 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 675 time to evaluate : 4.508 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8525 (mmt) cc_final: 0.8193 (mmt) REVERT: S 48 MET cc_start: 0.9186 (mtp) cc_final: 0.8887 (mtm) REVERT: V 8 LYS cc_start: 0.8358 (mttt) cc_final: 0.8074 (mtmm) REVERT: Y 99 ILE cc_start: 0.7321 (mt) cc_final: 0.6880 (tt) REVERT: Z 49 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7934 (mm-30) REVERT: a 103 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: a 114 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8933 (ptmm) REVERT: a 152 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8866 (ttmm) REVERT: b 93 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8062 (mttt) REVERT: b 119 LEU cc_start: 0.8630 (mm) cc_final: 0.8361 (mp) REVERT: d 25 SER cc_start: 0.7934 (OUTLIER) cc_final: 0.7729 (m) REVERT: e 63 ASP cc_start: 0.7177 (m-30) cc_final: 0.6743 (m-30) REVERT: g 16 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8660 (mt) REVERT: h 13 ASP cc_start: 0.8497 (t0) cc_final: 0.8002 (t0) REVERT: h 55 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: h 102 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: i 263 LYS cc_start: 0.8779 (ptpt) cc_final: 0.8575 (pttt) REVERT: j 85 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8205 (mttt) REVERT: l 411 MET cc_start: 0.8913 (mmp) cc_final: 0.8655 (mmp) REVERT: l 576 MET cc_start: 0.8715 (mtp) cc_final: 0.8452 (mtp) REVERT: m 99 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7386 (ttm) REVERT: m 135 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8235 (t80) REVERT: n 41 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8812 (mttm) REVERT: n 54 GLU cc_start: 0.7672 (pm20) cc_final: 0.7335 (mp0) REVERT: o 111 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8367 (ttpp) REVERT: p 59 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7820 (ptmt) REVERT: r 229 MET cc_start: 0.9385 (mtp) cc_final: 0.9168 (mtm) REVERT: r 302 MET cc_start: 0.9204 (mmp) cc_final: 0.8858 (mmp) REVERT: r 375 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9089 (tp) REVERT: s 206 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8435 (mp0) REVERT: s 227 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: s 296 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9140 (tt) REVERT: w 272 ASP cc_start: 0.8042 (m-30) cc_final: 0.7576 (m-30) REVERT: w 293 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7827 (ttp80) outliers start: 132 outliers final: 71 residues processed: 743 average time/residue: 1.6716 time to fit residues: 1485.4907 Evaluate side-chains 757 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 669 time to evaluate : 4.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 273 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 300 optimal weight: 0.5980 chunk 218 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 346 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN e 148 GLN f 73 ASN h 70 GLN i 47 ASN i 171 ASN i 186 HIS k 50 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 103 GLN u 77 HIS v 54 GLN w 107 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40726 Z= 0.253 Angle : 0.570 10.069 54936 Z= 0.284 Chirality : 0.042 0.196 5931 Planarity : 0.005 0.062 6684 Dihedral : 13.909 154.357 6572 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 3.22 % Allowed : 16.02 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 (0.12), residues: 4666 helix: 1.95 (0.09), residues: 2952 sheet: -0.58 (0.95), residues: 35 loop : -0.50 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.006 0.001 HIS S 27 PHE 0.028 0.001 PHE i 292 TYR 0.021 0.002 TYR r 406 ARG 0.019 0.000 ARG v 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 665 time to evaluate : 4.415 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8513 (mmt) cc_final: 0.8153 (mmt) REVERT: S 48 MET cc_start: 0.9194 (mtp) cc_final: 0.8902 (mtm) REVERT: U 16 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8008 (mm-30) REVERT: V 8 LYS cc_start: 0.8372 (mttt) cc_final: 0.8109 (mtmm) REVERT: V 106 ARG cc_start: 0.7127 (mtt90) cc_final: 0.6924 (mtt90) REVERT: Y 99 ILE cc_start: 0.7363 (mt) cc_final: 0.6910 (tt) REVERT: Z 49 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: a 103 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: a 114 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8996 (ptmm) REVERT: a 152 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8874 (ttmm) REVERT: b 93 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8072 (mttt) REVERT: d 25 SER cc_start: 0.7942 (OUTLIER) cc_final: 0.7739 (m) REVERT: d 36 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8472 (mt) REVERT: g 16 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8703 (mt) REVERT: h 13 ASP cc_start: 0.8545 (t0) cc_final: 0.8076 (t0) REVERT: h 55 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: h 102 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: j 85 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8196 (mttt) REVERT: l 411 MET cc_start: 0.8924 (mmp) cc_final: 0.8706 (mmp) REVERT: m 99 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7401 (ttm) REVERT: m 135 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8219 (t80) REVERT: n 41 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8818 (mttm) REVERT: n 54 GLU cc_start: 0.7684 (pm20) cc_final: 0.7345 (mp0) REVERT: p 59 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7829 (ptmt) REVERT: r 375 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9078 (tp) REVERT: s 206 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8451 (mp0) REVERT: s 227 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8357 (tp30) REVERT: s 296 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9123 (tt) REVERT: u 155 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7626 (pp20) REVERT: v 97 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8338 (mtpt) REVERT: w 45 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7854 (pp) REVERT: w 293 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7847 (ttp80) outliers start: 133 outliers final: 77 residues processed: 740 average time/residue: 1.6570 time to fit residues: 1471.8251 Evaluate side-chains 756 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 659 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 103 GLU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 335 LEU Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 170 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 401 optimal weight: 0.7980 chunk 422 optimal weight: 8.9990 chunk 385 optimal weight: 1.9990 chunk 411 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 371 optimal weight: 4.9990 chunk 389 optimal weight: 3.9990 chunk 409 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN e 148 GLN i 47 ASN ** i 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 50 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 255 ASN u 77 HIS v 54 GLN w 107 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40726 Z= 0.257 Angle : 0.579 13.969 54936 Z= 0.288 Chirality : 0.042 0.201 5931 Planarity : 0.005 0.061 6684 Dihedral : 13.802 154.299 6572 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 2.88 % Allowed : 16.61 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.55 (0.12), residues: 4666 helix: 1.91 (0.09), residues: 2951 sheet: -0.60 (0.95), residues: 35 loop : -0.51 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS S 27 PHE 0.028 0.001 PHE i 292 TYR 0.021 0.002 TYR r 406 ARG 0.012 0.000 ARG v 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 658 time to evaluate : 4.464 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8516 (mmt) cc_final: 0.8157 (mmt) REVERT: S 48 MET cc_start: 0.9195 (mtp) cc_final: 0.8906 (mtm) REVERT: V 8 LYS cc_start: 0.8376 (mttt) cc_final: 0.8129 (mtmm) REVERT: Y 99 ILE cc_start: 0.7353 (mt) cc_final: 0.6908 (tt) REVERT: Z 49 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: a 114 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.9002 (ptmm) REVERT: a 152 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8864 (ttmm) REVERT: d 25 SER cc_start: 0.7938 (OUTLIER) cc_final: 0.7722 (m) REVERT: d 73 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8086 (p0) REVERT: g 16 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8722 (mt) REVERT: h 13 ASP cc_start: 0.8554 (t0) cc_final: 0.8108 (t0) REVERT: h 55 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8571 (mt-10) REVERT: h 102 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7284 (pt0) REVERT: j 85 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8196 (mttt) REVERT: k 37 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8807 (mmt) REVERT: l 411 MET cc_start: 0.8918 (mmp) cc_final: 0.8706 (mmp) REVERT: m 99 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7402 (ttm) REVERT: m 135 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8199 (t80) REVERT: n 41 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8813 (mttm) REVERT: n 54 GLU cc_start: 0.7672 (pm20) cc_final: 0.7332 (mp0) REVERT: p 59 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7839 (ptmt) REVERT: r 229 MET cc_start: 0.9384 (mtp) cc_final: 0.9176 (mtm) REVERT: r 302 MET cc_start: 0.9249 (mmp) cc_final: 0.8898 (mmp) REVERT: r 375 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9069 (tp) REVERT: r 398 MET cc_start: 0.8397 (mmm) cc_final: 0.7783 (ttm) REVERT: s 206 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8451 (mp0) REVERT: s 227 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8347 (tp30) REVERT: s 296 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9117 (tt) REVERT: u 155 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7637 (pp20) REVERT: v 97 LYS cc_start: 0.8775 (mtmm) cc_final: 0.8341 (mtpt) REVERT: w 45 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7863 (pp) REVERT: w 293 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7851 (ttp80) outliers start: 119 outliers final: 76 residues processed: 727 average time/residue: 1.7113 time to fit residues: 1496.9155 Evaluate side-chains 744 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 649 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain h residue 18 MET Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 129 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 170 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain v residue 81 LYS Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 270 optimal weight: 0.6980 chunk 434 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 456 optimal weight: 0.9990 chunk 419 optimal weight: 4.9990 chunk 363 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 222 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN U 62 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN e 148 GLN i 47 ASN i 171 ASN k 50 ASN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS v 54 GLN w 107 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40726 Z= 0.200 Angle : 0.552 12.499 54936 Z= 0.275 Chirality : 0.040 0.188 5931 Planarity : 0.004 0.061 6684 Dihedral : 13.502 153.473 6572 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 2.40 % Allowed : 17.12 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.66 (0.12), residues: 4666 helix: 2.00 (0.09), residues: 2944 sheet: -0.47 (0.95), residues: 35 loop : -0.46 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.005 0.001 HIS S 27 PHE 0.028 0.001 PHE i 292 TYR 0.022 0.001 TYR r 406 ARG 0.012 0.000 ARG v 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 668 time to evaluate : 4.659 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8518 (mmt) cc_final: 0.8201 (mmt) REVERT: S 48 MET cc_start: 0.9187 (mtp) cc_final: 0.8893 (mtm) REVERT: U 82 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8574 (tttt) REVERT: V 8 LYS cc_start: 0.8364 (mttt) cc_final: 0.8104 (mtmm) REVERT: Z 49 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: a 114 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8995 (ptmm) REVERT: a 152 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8858 (ttmm) REVERT: b 93 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8063 (mttt) REVERT: d 25 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7702 (m) REVERT: d 73 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8049 (p0) REVERT: f 65 ASP cc_start: 0.8572 (m-30) cc_final: 0.8334 (m-30) REVERT: h 13 ASP cc_start: 0.8482 (t0) cc_final: 0.8076 (t0) REVERT: h 55 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8566 (mt-10) REVERT: h 102 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7228 (pt0) REVERT: j 85 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8193 (mttt) REVERT: k 37 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8806 (mmt) REVERT: l 411 MET cc_start: 0.8893 (mmp) cc_final: 0.8677 (mmp) REVERT: l 496 MET cc_start: 0.8286 (mmp) cc_final: 0.8046 (mmm) REVERT: m 99 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7361 (ttm) REVERT: n 41 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8809 (mttm) REVERT: n 54 GLU cc_start: 0.7654 (pm20) cc_final: 0.7301 (mp0) REVERT: o 111 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8346 (ttpp) REVERT: p 44 MET cc_start: 0.8840 (tpp) cc_final: 0.8440 (tpp) REVERT: p 59 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7746 (ptmt) REVERT: r 229 MET cc_start: 0.9382 (mtp) cc_final: 0.9127 (mtm) REVERT: r 302 MET cc_start: 0.9211 (mmp) cc_final: 0.8829 (mmp) REVERT: r 375 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9097 (tp) REVERT: s 206 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8444 (mp0) REVERT: s 227 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8333 (tp30) REVERT: s 296 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9128 (tt) REVERT: u 155 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7618 (pp20) REVERT: v 97 LYS cc_start: 0.8743 (mtmm) cc_final: 0.8308 (mtpt) REVERT: v 122 MET cc_start: 0.6264 (tpt) cc_final: 0.5979 (tpt) REVERT: w 293 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7815 (ttp80) outliers start: 99 outliers final: 67 residues processed: 722 average time/residue: 1.7010 time to fit residues: 1471.4742 Evaluate side-chains 743 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 659 time to evaluate : 4.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 110 ILE Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 52 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 152 LYS Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 25 SER Chi-restraints excluded: chain d residue 73 ASP Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 85 LYS Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 37 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 314 MET Chi-restraints excluded: chain l residue 373 LEU Chi-restraints excluded: chain l residue 446 ASN Chi-restraints excluded: chain l residue 482 MET Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 49 LEU Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 141 GLN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 170 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 216 SER Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 288 optimal weight: 0.9980 chunk 387 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 335 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 chunk 363 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 373 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 ASN ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 189 ASN e 148 GLN i 47 ASN i 171 ASN k 50 ASN l 59 GLN ** l 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS v 54 GLN w 107 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.110026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.090661 restraints weight = 52323.694| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.24 r_work: 0.2816 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 40726 Z= 0.153 Angle : 0.529 12.187 54936 Z= 0.262 Chirality : 0.039 0.177 5931 Planarity : 0.004 0.061 6684 Dihedral : 13.037 152.378 6571 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 1.89 % Allowed : 17.62 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.85 (0.13), residues: 4666 helix: 2.17 (0.10), residues: 2930 sheet: -0.31 (0.94), residues: 35 loop : -0.41 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.004 0.001 HIS i 112 PHE 0.029 0.001 PHE i 292 TYR 0.024 0.001 TYR r 406 ARG 0.011 0.000 ARG v 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19442.80 seconds wall clock time: 345 minutes 25.40 seconds (20725.40 seconds total)