Starting phenix.real_space_refine on Fri Feb 23 13:42:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyi_32206/02_2024/7vyi_32206_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyi_32206/02_2024/7vyi_32206.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyi_32206/02_2024/7vyi_32206_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyi_32206/02_2024/7vyi_32206_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyi_32206/02_2024/7vyi_32206_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyi_32206/02_2024/7vyi_32206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyi_32206/02_2024/7vyi_32206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyi_32206/02_2024/7vyi_32206_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyi_32206/02_2024/7vyi_32206_updated.pdb" } resolution = 3.1 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 27 5.49 5 S 285 5.16 5 C 25334 2.51 5 N 6186 2.21 5 O 6788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "U PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d GLU 128": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "l GLU 559": "OE1" <-> "OE2" Residue "m PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "o GLU 22": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "p GLU 70": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "p GLU 92": "OE1" <-> "OE2" Residue "p GLU 142": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "u GLU 153": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 185": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38620 Number of models: 1 Model: "" Number of chains: 41 Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 333 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 949 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1161 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 129} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1303 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4785 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 28, 'TRANS': 574} Chain: "m" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 951 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "n" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 456 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 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: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1530 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "w" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2563 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "i" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "j" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 146 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "m" 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: "r" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 354 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {' UQ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-11': 1, ' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 35 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 20.30, per 1000 atoms: 0.53 Number of scatterers: 38620 At special positions: 0 Unit cell: (178.317, 194.43, 137.498, 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 285 16.00 P 27 15.00 O 6788 8.00 N 6186 7.00 C 25334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.02 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.04 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.04 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: 14.69 Conformation dependent library (CDL) restraints added in 6.8 seconds 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 197 helices and 3 sheets defined 63.0% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.92 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.018A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 29 Proline residue: S 7 - end of helix removed outlier: 3.896A pdb=" N ILE S 18 " --> pdb=" O CYS S 15 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 43 through 55 Processing helix chain 'S' and resid 66 through 69 Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 removed outlier: 3.668A pdb=" N THR V 121 " --> pdb=" O TYR V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 99 Proline residue: W 73 - end of helix removed outlier: 3.705A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 124 No H-bonds generated for 'chain 'W' and resid 121 through 124' Processing helix chain 'W' and resid 130 through 142 removed outlier: 6.339A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.728A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 78 through 81 No H-bonds generated for 'chain 'Y' and resid 78 through 81' Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 29 through 37 Processing helix chain 'Z' and resid 47 through 53 removed outlier: 4.905A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 89 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 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 25 Processing helix chain 'b' and resid 65 through 73 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.487A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 116 Processing helix chain 'd' and resid 118 through 124 removed outlier: 3.508A pdb=" N TYR d 121 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG d 122 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN d 124 " --> pdb=" O TYR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 175 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 3.567A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 115 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 73 Processing helix chain 'g' and resid 4 through 6 No H-bonds generated for 'chain 'g' and resid 4 through 6' 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 Processing helix chain 'g' and resid 111 through 113 No H-bonds generated for 'chain 'g' and resid 111 through 113' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 99 Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 removed outlier: 3.573A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.119A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.893A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.896A 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: 4.013A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.343A 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: 3.875A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.213A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.910A 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 340 through 345 Processing helix chain 'j' and resid 2 through 26 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.841A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 26 through 50 Processing helix chain 'k' and resid 54 through 85 removed outlier: 3.634A 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 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 14 removed outlier: 3.870A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 23 removed outlier: 4.666A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 28 No H-bonds generated for 'chain 'l' and resid 26 through 28' Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.330A 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: 3.896A 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 removed outlier: 3.543A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.916A 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: 4.233A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 250 removed outlier: 3.576A pdb=" N HIS l 248 " --> pdb=" O SER l 244 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER l 249 " --> pdb=" O ALA l 245 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER l 250 " --> pdb=" O LEU l 246 " (cutoff:3.500A) Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 267 No H-bonds generated for 'chain 'l' and resid 264 through 267' Processing helix chain 'l' and resid 272 through 294 removed outlier: 4.373A 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 350 removed outlier: 3.686A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.793A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 Processing helix chain 'l' and resid 448 through 471 removed outlier: 3.575A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.173A 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: 3.723A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 547 removed outlier: 3.518A pdb=" N TYR l 529 " --> pdb=" O LEU l 526 " (cutoff:3.500A) Proline residue: l 530 - end of helix removed outlier: 4.236A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU l 536 " --> pdb=" O MET l 533 " (cutoff:3.500A) Proline residue: l 537 - end of helix 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 removed outlier: 3.590A pdb=" N MET l 599 " --> pdb=" O ILE l 595 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR l 600 " --> pdb=" O MET l 596 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 4.128A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.258A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 11 No H-bonds generated for 'chain 'n' and resid 8 through 11' Processing helix chain 'n' and resid 14 through 38 Proline residue: n 18 - end of helix removed outlier: 3.933A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR n 36 " --> pdb=" O ASP n 32 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ALA n 37 " --> pdb=" O GLU n 33 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 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 49 Processing helix chain 'p' and resid 57 through 73 removed outlier: 4.063A pdb=" N GLN p 62 " --> pdb=" O VAL p 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU p 64 " --> pdb=" O ALA p 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU p 69 " --> pdb=" O ARG p 65 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR p 73 " --> pdb=" O GLU p 69 " (cutoff:3.500A) 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 143 removed outlier: 3.828A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix removed outlier: 4.206A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.184A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.829A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.481A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.576A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.276A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.207A 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 140 through 170 removed outlier: 4.130A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (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: 3.981A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.207A 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 248 removed outlier: 4.904A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.249A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.758A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) 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: 3.754A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 4.093A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 3 through 32 Proline residue: s 12 - end of helix removed outlier: 3.875A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG s 25 " --> pdb=" O THR s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.370A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 4.212A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.738A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.587A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 310 removed outlier: 5.177A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 13 Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 101 through 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 27 through 29 No H-bonds generated for 'chain 'v' and resid 27 through 29' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 77 through 79 No H-bonds generated for 'chain 'v' and resid 77 through 79' Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.654A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 93 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.093A 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 250 Processing helix chain 'w' and resid 261 through 263 No H-bonds generated for 'chain 'w' and resid 261 through 263' Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 3.881A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= B, first strand: chain 'l' and resid 62 through 67 removed outlier: 3.663A pdb=" N ASN l 65 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.678A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 1998 hydrogen bonds defined for protein. 5664 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: 12.00 Time building geometry restraints manager: 15.94 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: 5862 1.31 - 1.44: 10766 1.44 - 1.57: 22354 1.57 - 1.70: 126 1.70 - 1.83: 515 Bond restraints: 39623 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C18 UQ s 401 " pdb=" C19 UQ s 401 " 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 401 " pdb=" C14 UQ s 401 " ideal model delta sigma weight residual 1.335 1.549 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C8 UQ s 401 " pdb=" C9 UQ s 401 " ideal model delta sigma weight residual 1.334 1.541 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C4' ADP w 401 " pdb=" O4' ADP w 401 " ideal model delta sigma weight residual 1.426 1.618 -0.192 2.00e-02 2.50e+03 9.26e+01 ... (remaining 39618 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.36: 1100 105.36 - 112.65: 21069 112.65 - 119.93: 13879 119.93 - 127.22: 16910 127.22 - 134.51: 598 Bond angle restraints: 53556 Sorted by residual: angle pdb=" C TYR c 75 " pdb=" N PRO c 76 " pdb=" CA PRO c 76 " ideal model delta sigma weight residual 119.85 130.15 -10.30 1.01e+00 9.80e-01 1.04e+02 angle pdb=" C PHE c 37 " pdb=" N PRO c 38 " pdb=" CA PRO c 38 " ideal model delta sigma weight residual 119.89 127.10 -7.21 1.02e+00 9.61e-01 4.99e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.53 -9.20 1.32e+00 5.72e-01 4.85e+01 angle pdb=" C11 CDL i 401 " pdb=" CA5 CDL i 401 " pdb=" OA6 CDL i 401 " ideal model delta sigma weight residual 111.33 120.31 -8.98 1.32e+00 5.72e-01 4.61e+01 angle pdb=" C51 CDL g 202 " pdb=" CB5 CDL g 202 " pdb=" OB6 CDL g 202 " ideal model delta sigma weight residual 111.33 120.19 -8.86 1.32e+00 5.72e-01 4.49e+01 ... (remaining 53551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.24: 22900 32.24 - 64.49: 965 64.49 - 96.73: 86 96.73 - 128.98: 16 128.98 - 161.22: 11 Dihedral angle restraints: 23978 sinusoidal: 10340 harmonic: 13638 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 87.62 -147.61 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O2A ADP w 401 " pdb=" O3A ADP w 401 " pdb=" PA ADP w 401 " pdb=" PB ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 -167.08 107.08 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O1B ADP w 401 " pdb=" O3A ADP w 401 " pdb=" PB ADP w 401 " pdb=" PA ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 35.96 -95.97 1 2.00e+01 2.50e-03 2.65e+01 ... (remaining 23975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5357 0.071 - 0.142: 455 0.142 - 0.213: 16 0.213 - 0.284: 1 0.284 - 0.356: 2 Chirality restraints: 5831 Sorted by residual: chirality pdb=" CA LEU w 246 " pdb=" N LEU w 246 " pdb=" C LEU w 246 " pdb=" CB LEU w 246 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA LYS w 243 " pdb=" N LYS w 243 " pdb=" C LYS w 243 " pdb=" CB LYS w 243 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CB ILE i 86 " pdb=" CA ILE i 86 " pdb=" CG1 ILE i 86 " pdb=" CG2 ILE i 86 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 5828 not shown) Planarity restraints: 6553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 401 " -0.088 2.00e-02 2.50e+03 4.45e-01 2.48e+03 pdb=" C11 UQ s 401 " -0.412 2.00e-02 2.50e+03 pdb=" C7 UQ s 401 " -0.521 2.00e-02 2.50e+03 pdb=" C8 UQ s 401 " 0.613 2.00e-02 2.50e+03 pdb=" C9 UQ s 401 " 0.408 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 401 " -0.158 2.00e-02 2.50e+03 2.05e-01 5.23e+02 pdb=" C18 UQ s 401 " 0.092 2.00e-02 2.50e+03 pdb=" C19 UQ s 401 " 0.347 2.00e-02 2.50e+03 pdb=" C20 UQ s 401 " -0.051 2.00e-02 2.50e+03 pdb=" C21 UQ s 401 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 401 " 0.155 2.00e-02 2.50e+03 2.03e-01 5.15e+02 pdb=" C13 UQ s 401 " -0.084 2.00e-02 2.50e+03 pdb=" C14 UQ s 401 " -0.348 2.00e-02 2.50e+03 pdb=" C15 UQ s 401 " 0.050 2.00e-02 2.50e+03 pdb=" C16 UQ s 401 " 0.228 2.00e-02 2.50e+03 ... (remaining 6550 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2511 2.74 - 3.28: 39255 3.28 - 3.82: 65741 3.82 - 4.36: 78890 4.36 - 4.90: 136249 Nonbonded interactions: 322646 Sorted by model distance: nonbonded pdb=" O ILE l 556 " pdb=" OG1 THR l 560 " model vdw 2.196 2.440 nonbonded pdb=" OE2 GLU r 123 " pdb=" OG SER r 157 " model vdw 2.201 2.440 nonbonded pdb=" O ASP Q 68 " pdb=" ND2 ASN i 49 " model vdw 2.206 2.520 nonbonded pdb=" OD1 ASP X 111 " pdb=" N SER X 112 " model vdw 2.208 2.520 nonbonded pdb=" OG SER w 123 " pdb=" OD1 ASP w 125 " model vdw 2.216 2.440 ... (remaining 322641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.080 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 98.430 Find NCS groups from input model: 1.250 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.006 0.225 39623 Z= 0.424 Angle : 0.779 16.836 53556 Z= 0.393 Chirality : 0.040 0.356 5831 Planarity : 0.008 0.445 6553 Dihedral : 17.311 161.221 15146 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 0.32 % Allowed : 0.35 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.13), residues: 4586 helix: 2.12 (0.10), residues: 2915 sheet: -0.56 (1.21), residues: 23 loop : -0.41 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.005 0.001 HIS r 220 PHE 0.031 0.001 PHE i 292 TYR 0.042 0.001 TYR w 129 ARG 0.009 0.000 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 837 time to evaluate : 4.455 Fit side-chains revert: symmetry clash REVERT: V 44 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6917 (pttt) REVERT: V 60 THR cc_start: 0.8173 (m) cc_final: 0.7951 (m) REVERT: V 100 THR cc_start: 0.8608 (p) cc_final: 0.8403 (p) REVERT: X 74 LEU cc_start: 0.8641 (pt) cc_final: 0.8367 (pt) REVERT: Y 65 MET cc_start: 0.8746 (tmm) cc_final: 0.8458 (ttt) REVERT: Z 61 VAL cc_start: 0.8669 (m) cc_final: 0.8342 (p) REVERT: b 76 LEU cc_start: 0.9162 (tp) cc_final: 0.8954 (tp) REVERT: k 27 MET cc_start: 0.7722 (tpp) cc_final: 0.7424 (tpp) REVERT: m 5 ILE cc_start: 0.7961 (tt) cc_final: 0.7683 (tt) REVERT: p 64 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8479 (tt) REVERT: p 65 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7480 (ttt180) REVERT: p 66 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: s 24 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: s 121 TRP cc_start: 0.7525 (t60) cc_final: 0.7261 (t60) outliers start: 13 outliers final: 5 residues processed: 846 average time/residue: 0.5116 time to fit residues: 698.4628 Evaluate side-chains 754 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 745 time to evaluate : 4.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 103 GLU Chi-restraints excluded: chain o residue 22 GLU Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 62 GLN Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 65 ARG Chi-restraints excluded: chain p residue 66 GLN Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 0.9980 chunk 343 optimal weight: 0.5980 chunk 190 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 355 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 264 optimal weight: 0.0970 chunk 411 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 46 GLN d 134 GLN l 135 ASN ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN p 12 HIS p 33 HIS p 66 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 83 HIS r 103 GLN r 251 ASN r 304 GLN u 16 GLN u 77 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 39623 Z= 0.145 Angle : 0.523 13.218 53556 Z= 0.254 Chirality : 0.038 0.195 5831 Planarity : 0.004 0.048 6553 Dihedral : 15.104 150.265 6096 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 0.91 % Allowed : 6.57 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.13), residues: 4586 helix: 2.27 (0.10), residues: 2912 sheet: -0.58 (1.23), residues: 23 loop : -0.35 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.011 0.001 HIS h 27 PHE 0.030 0.001 PHE i 292 TYR 0.031 0.001 TYR l 422 ARG 0.003 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 772 time to evaluate : 4.345 Fit side-chains revert: symmetry clash REVERT: V 44 LYS cc_start: 0.7351 (mmtt) cc_final: 0.7107 (pttt) REVERT: X 74 LEU cc_start: 0.8689 (pt) cc_final: 0.8406 (pt) REVERT: Z 61 VAL cc_start: 0.8686 (m) cc_final: 0.8338 (p) REVERT: g 36 MET cc_start: 0.8384 (mmm) cc_final: 0.7944 (mmm) REVERT: i 49 ASN cc_start: 0.7672 (p0) cc_final: 0.7470 (p0) REVERT: i 100 MET cc_start: 0.8132 (mmp) cc_final: 0.7920 (mmp) REVERT: k 27 MET cc_start: 0.7719 (tpp) cc_final: 0.7330 (tpp) REVERT: l 128 MET cc_start: 0.8745 (tpt) cc_final: 0.8068 (tpt) REVERT: l 401 MET cc_start: 0.7833 (mmm) cc_final: 0.7544 (mmm) REVERT: m 173 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7858 (ttm-80) REVERT: p 43 LEU cc_start: 0.8867 (tt) cc_final: 0.8644 (mt) REVERT: p 64 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8303 (tp) outliers start: 37 outliers final: 26 residues processed: 788 average time/residue: 0.5086 time to fit residues: 652.9825 Evaluate side-chains 753 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 726 time to evaluate : 4.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 0.0070 chunk 342 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 113 optimal weight: 0.0770 chunk 412 optimal weight: 0.0170 chunk 445 optimal weight: 0.8980 chunk 367 optimal weight: 1.9990 chunk 408 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 330 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 46 GLN l 135 ASN ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 400 ASN ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN p 33 HIS ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 83 HIS r 103 GLN s 235 ASN u 77 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 39623 Z= 0.149 Angle : 0.504 12.442 53556 Z= 0.247 Chirality : 0.038 0.169 5831 Planarity : 0.004 0.047 6553 Dihedral : 13.925 159.144 6073 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 1.04 % Allowed : 8.47 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.13), residues: 4586 helix: 2.33 (0.10), residues: 2917 sheet: -0.57 (1.22), residues: 23 loop : -0.33 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS r 83 PHE 0.029 0.001 PHE i 292 TYR 0.027 0.001 TYR l 422 ARG 0.007 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 749 time to evaluate : 4.717 Fit side-chains REVERT: V 44 LYS cc_start: 0.7482 (mmtt) cc_final: 0.7210 (pttt) REVERT: X 74 LEU cc_start: 0.8698 (pt) cc_final: 0.8423 (pt) REVERT: Z 61 VAL cc_start: 0.8658 (m) cc_final: 0.8335 (p) REVERT: g 36 MET cc_start: 0.8397 (mmm) cc_final: 0.7983 (mmm) REVERT: g 89 ASP cc_start: 0.8642 (m-30) cc_final: 0.8427 (m-30) REVERT: i 281 LEU cc_start: 0.7917 (mp) cc_final: 0.7701 (mp) REVERT: k 27 MET cc_start: 0.7812 (tpp) cc_final: 0.7427 (tpp) REVERT: l 128 MET cc_start: 0.8761 (tpt) cc_final: 0.8225 (tpt) REVERT: l 401 MET cc_start: 0.7839 (mmm) cc_final: 0.7558 (mmm) REVERT: m 173 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7811 (ttm-80) REVERT: p 64 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8472 (tp) outliers start: 42 outliers final: 32 residues processed: 772 average time/residue: 0.5122 time to fit residues: 640.0252 Evaluate side-chains 752 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 719 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 77 CYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 6.9990 chunk 309 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 196 optimal weight: 0.1980 chunk 276 optimal weight: 0.9990 chunk 413 optimal weight: 6.9990 chunk 437 optimal weight: 0.4980 chunk 216 optimal weight: 2.9990 chunk 391 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 27 HIS ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 83 HIS r 103 GLN r 169 ASN r 192 ASN u 77 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39623 Z= 0.189 Angle : 0.518 11.308 53556 Z= 0.255 Chirality : 0.039 0.173 5831 Planarity : 0.004 0.048 6553 Dihedral : 13.252 149.325 6073 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 1.43 % Allowed : 9.61 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.13), residues: 4586 helix: 2.29 (0.10), residues: 2921 sheet: -0.43 (1.26), residues: 23 loop : -0.32 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS r 83 PHE 0.030 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.007 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 734 time to evaluate : 4.003 Fit side-chains REVERT: V 44 LYS cc_start: 0.7501 (mmtt) cc_final: 0.7227 (pttt) REVERT: X 74 LEU cc_start: 0.8722 (pt) cc_final: 0.8401 (pt) REVERT: Z 61 VAL cc_start: 0.8672 (m) cc_final: 0.8350 (p) REVERT: i 282 MET cc_start: 0.8342 (mtt) cc_final: 0.8083 (mtp) REVERT: k 27 MET cc_start: 0.7901 (tpp) cc_final: 0.7504 (tpp) REVERT: k 89 TYR cc_start: 0.8247 (m-80) cc_final: 0.7968 (m-80) REVERT: l 401 MET cc_start: 0.7873 (mmm) cc_final: 0.7517 (mmm) REVERT: m 173 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7876 (ttm-80) REVERT: p 64 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8488 (tp) REVERT: s 233 MET cc_start: 0.8316 (tmm) cc_final: 0.7677 (tmm) REVERT: v 39 MET cc_start: 0.6117 (mmm) cc_final: 0.5916 (mmm) REVERT: w 248 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6140 (mm-30) outliers start: 58 outliers final: 43 residues processed: 765 average time/residue: 0.5164 time to fit residues: 642.6936 Evaluate side-chains 762 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 718 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 13 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 326 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 373 optimal weight: 4.9990 chunk 302 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 393 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 226 GLN ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 83 HIS r 103 GLN r 220 HIS u 77 HIS w 235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39623 Z= 0.166 Angle : 0.506 10.928 53556 Z= 0.250 Chirality : 0.039 0.193 5831 Planarity : 0.004 0.047 6553 Dihedral : 12.749 136.634 6073 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 1.51 % Allowed : 10.38 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.13), residues: 4586 helix: 2.33 (0.10), residues: 2920 sheet: -0.43 (1.27), residues: 23 loop : -0.31 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS r 83 PHE 0.030 0.001 PHE i 292 TYR 0.023 0.001 TYR l 422 ARG 0.007 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 742 time to evaluate : 4.377 Fit side-chains REVERT: V 44 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7230 (pttt) REVERT: X 74 LEU cc_start: 0.8723 (pt) cc_final: 0.8427 (pt) REVERT: X 77 GLU cc_start: 0.7733 (tp30) cc_final: 0.7451 (tp30) REVERT: Y 46 GLN cc_start: 0.8412 (mt0) cc_final: 0.8178 (mt0) REVERT: Z 61 VAL cc_start: 0.8636 (m) cc_final: 0.8311 (p) REVERT: i 282 MET cc_start: 0.8429 (mtt) cc_final: 0.8188 (mtp) REVERT: k 27 MET cc_start: 0.7895 (tpp) cc_final: 0.7568 (tpp) REVERT: l 186 MET cc_start: 0.8950 (ttm) cc_final: 0.8644 (ttp) REVERT: l 340 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: l 401 MET cc_start: 0.7804 (mmm) cc_final: 0.7405 (mmm) REVERT: m 173 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7876 (ttm-80) REVERT: p 64 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8469 (tp) REVERT: r 256 TYR cc_start: 0.7965 (p90) cc_final: 0.7704 (p90) REVERT: s 233 MET cc_start: 0.8334 (tmm) cc_final: 0.7780 (tmm) outliers start: 61 outliers final: 44 residues processed: 779 average time/residue: 0.5363 time to fit residues: 685.5526 Evaluate side-chains 766 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 720 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 6.9990 chunk 394 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 438 optimal weight: 8.9990 chunk 363 optimal weight: 0.9990 chunk 202 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 83 HIS l 135 ASN ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 83 HIS r 103 GLN ** r 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39623 Z= 0.207 Angle : 0.530 11.381 53556 Z= 0.261 Chirality : 0.040 0.200 5831 Planarity : 0.004 0.048 6553 Dihedral : 12.418 125.802 6073 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 1.73 % Allowed : 10.62 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.13), residues: 4586 helix: 2.29 (0.10), residues: 2920 sheet: -0.49 (1.29), residues: 23 loop : -0.32 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.010 0.001 HIS r 83 PHE 0.031 0.001 PHE i 292 TYR 0.019 0.001 TYR r 406 ARG 0.007 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 724 time to evaluate : 4.675 Fit side-chains REVERT: V 44 LYS cc_start: 0.7545 (mmtt) cc_final: 0.7242 (pttt) REVERT: V 104 ARG cc_start: 0.7272 (mmm160) cc_final: 0.7057 (mmm160) REVERT: X 74 LEU cc_start: 0.8712 (pt) cc_final: 0.8437 (pt) REVERT: Y 46 GLN cc_start: 0.8468 (mt0) cc_final: 0.8258 (mt0) REVERT: Z 61 VAL cc_start: 0.8633 (m) cc_final: 0.8307 (p) REVERT: e 67 TYR cc_start: 0.9131 (m-80) cc_final: 0.8919 (m-10) REVERT: g 36 MET cc_start: 0.8499 (mmm) cc_final: 0.8074 (mmm) REVERT: i 69 MET cc_start: 0.8176 (mtm) cc_final: 0.7924 (mtm) REVERT: i 282 MET cc_start: 0.8495 (mtt) cc_final: 0.8264 (mtp) REVERT: k 27 MET cc_start: 0.7916 (tpp) cc_final: 0.7561 (tpp) REVERT: k 89 TYR cc_start: 0.8208 (m-80) cc_final: 0.7776 (m-80) REVERT: l 340 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8787 (m-80) REVERT: l 401 MET cc_start: 0.7881 (mmm) cc_final: 0.7452 (mtm) REVERT: m 137 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8327 (t) REVERT: m 173 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7918 (ttm-80) REVERT: n 53 GLU cc_start: 0.7465 (tt0) cc_final: 0.6952 (tt0) REVERT: o 70 TYR cc_start: 0.9236 (t80) cc_final: 0.8967 (t80) REVERT: r 256 TYR cc_start: 0.8000 (p90) cc_final: 0.7738 (p90) REVERT: v 68 LYS cc_start: 0.8847 (tttm) cc_final: 0.8635 (tttm) outliers start: 70 outliers final: 56 residues processed: 768 average time/residue: 0.5099 time to fit residues: 634.2610 Evaluate side-chains 769 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 711 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 152 LYS Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 558 LEU Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 345 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 320 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 368 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 436 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 266 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 135 ASN ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 83 HIS r 103 GLN r 220 HIS ** r 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39623 Z= 0.178 Angle : 0.520 11.869 53556 Z= 0.256 Chirality : 0.039 0.203 5831 Planarity : 0.004 0.048 6553 Dihedral : 12.076 123.006 6071 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 1.68 % Allowed : 11.26 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.13), residues: 4586 helix: 2.30 (0.10), residues: 2923 sheet: -0.52 (1.29), residues: 23 loop : -0.29 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.010 0.001 HIS r 83 PHE 0.030 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.006 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 731 time to evaluate : 4.226 Fit side-chains REVERT: V 44 LYS cc_start: 0.7595 (mmtt) cc_final: 0.7245 (pttt) REVERT: V 62 THR cc_start: 0.7793 (m) cc_final: 0.7499 (m) REVERT: X 74 LEU cc_start: 0.8702 (pt) cc_final: 0.8412 (pt) REVERT: Y 46 GLN cc_start: 0.8467 (mt0) cc_final: 0.8247 (mt0) REVERT: Z 61 VAL cc_start: 0.8630 (m) cc_final: 0.8310 (p) REVERT: k 27 MET cc_start: 0.7900 (tpp) cc_final: 0.7601 (tpp) REVERT: l 186 MET cc_start: 0.8970 (ttm) cc_final: 0.8575 (ttp) REVERT: l 340 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8769 (m-80) REVERT: l 401 MET cc_start: 0.7889 (mmm) cc_final: 0.7417 (mtm) REVERT: m 137 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8337 (t) REVERT: m 173 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7931 (ttm-80) REVERT: n 53 GLU cc_start: 0.7424 (tt0) cc_final: 0.6901 (tt0) REVERT: r 256 TYR cc_start: 0.7993 (p90) cc_final: 0.7729 (p90) REVERT: s 233 MET cc_start: 0.8305 (tmm) cc_final: 0.8085 (tmm) REVERT: v 68 LYS cc_start: 0.8840 (tttm) cc_final: 0.8607 (tttm) REVERT: v 76 ASN cc_start: 0.8235 (t0) cc_final: 0.7799 (p0) outliers start: 68 outliers final: 56 residues processed: 770 average time/residue: 0.5068 time to fit residues: 633.0991 Evaluate side-chains 783 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 725 time to evaluate : 4.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 558 LEU Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain v residue 28 ASP Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 260 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 297 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 343 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 83 HIS l 135 ASN ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 83 HIS r 103 GLN ** r 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS v 85 HIS w 127 ASN ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39623 Z= 0.174 Angle : 0.520 12.095 53556 Z= 0.256 Chirality : 0.039 0.201 5831 Planarity : 0.004 0.048 6553 Dihedral : 11.868 120.343 6071 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.97 % Rotamer: Outliers : 1.80 % Allowed : 11.26 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.13), residues: 4586 helix: 2.31 (0.10), residues: 2925 sheet: -0.55 (1.29), residues: 23 loop : -0.27 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.010 0.001 HIS r 83 PHE 0.030 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.007 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 728 time to evaluate : 4.328 Fit side-chains REVERT: V 44 LYS cc_start: 0.7646 (mmtt) cc_final: 0.7244 (pttt) REVERT: V 62 THR cc_start: 0.7796 (m) cc_final: 0.7501 (m) REVERT: X 74 LEU cc_start: 0.8697 (pt) cc_final: 0.8404 (pt) REVERT: Z 61 VAL cc_start: 0.8632 (m) cc_final: 0.8314 (p) REVERT: k 89 TYR cc_start: 0.8212 (m-80) cc_final: 0.7796 (m-80) REVERT: l 186 MET cc_start: 0.8974 (ttm) cc_final: 0.8619 (ttp) REVERT: l 340 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8783 (m-80) REVERT: l 401 MET cc_start: 0.7891 (mmm) cc_final: 0.7432 (mtm) REVERT: m 137 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8365 (t) REVERT: m 173 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7929 (ttm-80) REVERT: n 53 GLU cc_start: 0.7433 (tt0) cc_final: 0.6904 (tt0) REVERT: r 256 TYR cc_start: 0.7994 (p90) cc_final: 0.7736 (p90) REVERT: v 68 LYS cc_start: 0.8837 (tttm) cc_final: 0.8607 (tttm) REVERT: v 76 ASN cc_start: 0.8163 (t0) cc_final: 0.7763 (p0) outliers start: 73 outliers final: 58 residues processed: 771 average time/residue: 0.5043 time to fit residues: 633.7611 Evaluate side-chains 776 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 716 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 558 LEU Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain v residue 28 ASP Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 285 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 0.9990 chunk 418 optimal weight: 0.9990 chunk 381 optimal weight: 0.4980 chunk 406 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 319 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 367 optimal weight: 0.4980 chunk 384 optimal weight: 3.9990 chunk 405 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 83 HIS d 140 GLN l 135 ASN ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 44 GLN r 83 HIS ** r 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 39623 Z= 0.165 Angle : 0.521 12.602 53556 Z= 0.257 Chirality : 0.038 0.205 5831 Planarity : 0.004 0.048 6553 Dihedral : 11.689 118.951 6069 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 1.61 % Allowed : 11.44 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.13), residues: 4586 helix: 2.34 (0.10), residues: 2919 sheet: -0.55 (1.29), residues: 23 loop : -0.26 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.010 0.001 HIS r 83 PHE 0.029 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.007 0.000 ARG w 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 730 time to evaluate : 4.785 Fit side-chains REVERT: V 44 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7233 (pttt) REVERT: V 62 THR cc_start: 0.7726 (m) cc_final: 0.7424 (m) REVERT: X 74 LEU cc_start: 0.8684 (pt) cc_final: 0.8379 (pt) REVERT: Y 46 GLN cc_start: 0.8449 (mt0) cc_final: 0.8228 (mt0) REVERT: Z 61 VAL cc_start: 0.8653 (m) cc_final: 0.8342 (p) REVERT: k 26 LEU cc_start: 0.7688 (tp) cc_final: 0.7480 (tp) REVERT: k 89 TYR cc_start: 0.8050 (m-80) cc_final: 0.7598 (m-80) REVERT: l 186 MET cc_start: 0.8961 (ttm) cc_final: 0.8631 (ttp) REVERT: l 340 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8782 (m-80) REVERT: l 401 MET cc_start: 0.7885 (mmm) cc_final: 0.7657 (mtt) REVERT: m 137 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8396 (t) REVERT: m 173 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7913 (ttm-80) REVERT: n 53 GLU cc_start: 0.7425 (tt0) cc_final: 0.6911 (tt0) REVERT: s 156 MET cc_start: 0.7728 (tpt) cc_final: 0.7487 (tpt) REVERT: v 68 LYS cc_start: 0.8843 (tttm) cc_final: 0.8617 (tttm) REVERT: v 76 ASN cc_start: 0.7973 (t0) cc_final: 0.7645 (p0) REVERT: v 105 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7309 (tm-30) outliers start: 65 outliers final: 56 residues processed: 767 average time/residue: 0.5144 time to fit residues: 642.8838 Evaluate side-chains 779 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 720 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 558 LEU Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 0.7980 chunk 430 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 299 optimal weight: 3.9990 chunk 451 optimal weight: 5.9990 chunk 415 optimal weight: 0.0070 chunk 359 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 220 optimal weight: 0.0570 overall best weight: 1.1518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 83 HIS ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN r 83 HIS r 220 HIS ** r 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39623 Z= 0.197 Angle : 0.537 13.152 53556 Z= 0.265 Chirality : 0.039 0.205 5831 Planarity : 0.004 0.048 6553 Dihedral : 11.616 119.078 6069 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.86 % Rotamer: Outliers : 1.63 % Allowed : 11.51 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.13), residues: 4586 helix: 2.28 (0.10), residues: 2924 sheet: -0.48 (1.31), residues: 23 loop : -0.27 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.011 0.001 HIS r 83 PHE 0.031 0.001 PHE i 292 TYR 0.019 0.001 TYR r 406 ARG 0.006 0.000 ARG w 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 723 time to evaluate : 4.442 Fit side-chains REVERT: V 44 LYS cc_start: 0.7664 (mmtt) cc_final: 0.7273 (pttt) REVERT: X 74 LEU cc_start: 0.8713 (pt) cc_final: 0.8413 (pt) REVERT: Y 46 GLN cc_start: 0.8482 (mt0) cc_final: 0.8242 (mt0) REVERT: Z 61 VAL cc_start: 0.8683 (m) cc_final: 0.8342 (p) REVERT: i 282 MET cc_start: 0.8528 (mtt) cc_final: 0.8299 (mtp) REVERT: k 26 LEU cc_start: 0.7746 (tp) cc_final: 0.7510 (tp) REVERT: k 89 TYR cc_start: 0.8228 (m-80) cc_final: 0.7769 (m-80) REVERT: l 186 MET cc_start: 0.8958 (ttm) cc_final: 0.8640 (ttp) REVERT: l 340 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8793 (m-80) REVERT: l 401 MET cc_start: 0.7911 (mmm) cc_final: 0.7668 (mtt) REVERT: m 137 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8497 (t) REVERT: m 173 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7928 (ttm-80) REVERT: n 53 GLU cc_start: 0.7439 (tt0) cc_final: 0.6914 (tt0) REVERT: r 256 TYR cc_start: 0.8021 (p90) cc_final: 0.7758 (p90) REVERT: s 121 TRP cc_start: 0.7513 (t60) cc_final: 0.6961 (t60) REVERT: s 156 MET cc_start: 0.7718 (tpt) cc_final: 0.7485 (tpt) REVERT: v 105 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7336 (tm-30) outliers start: 66 outliers final: 60 residues processed: 760 average time/residue: 0.5149 time to fit residues: 638.0377 Evaluate side-chains 769 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 706 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain W residue 114 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain Y residue 65 MET Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 225 THR Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 340 PHE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 558 LEU Chi-restraints excluded: chain m residue 10 SER Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 137 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 43 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 152 GLU Chi-restraints excluded: chain r residue 43 ASN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 184 HIS Chi-restraints excluded: chain r residue 253 LEU Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 53 LEU Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 121 ASP Chi-restraints excluded: chain u residue 126 SER Chi-restraints excluded: chain v residue 28 ASP Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 163 ILE Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 0.9990 chunk 382 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 331 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 359 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 369 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 83 HIS ** r 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 HIS ** w 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.099493 restraints weight = 54186.577| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.39 r_work: 0.2933 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 39623 Z= 0.235 Angle : 0.645 59.200 53556 Z= 0.345 Chirality : 0.040 0.293 5831 Planarity : 0.004 0.048 6553 Dihedral : 11.619 119.088 6069 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.10 % Favored : 95.88 % Rotamer: Outliers : 1.58 % Allowed : 11.71 % Favored : 86.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.13), residues: 4586 helix: 2.28 (0.10), residues: 2923 sheet: -0.48 (1.31), residues: 23 loop : -0.28 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.010 0.001 HIS r 83 PHE 0.031 0.001 PHE i 292 TYR 0.019 0.001 TYR r 406 ARG 0.006 0.000 ARG w 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11348.11 seconds wall clock time: 204 minutes 57.45 seconds (12297.45 seconds total)