Starting phenix.real_space_refine on Tue Apr 16 10:40:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vye_32202/04_2024/7vye_32202_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vye_32202/04_2024/7vye_32202.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vye_32202/04_2024/7vye_32202_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/7vye_32202/04_2024/7vye_32202_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vye_32202/04_2024/7vye_32202_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vye_32202/04_2024/7vye_32202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vye_32202/04_2024/7vye_32202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vye_32202/04_2024/7vye_32202_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vye_32202/04_2024/7vye_32202_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 31 5.49 5 S 285 5.16 5 C 25492 2.51 5 N 6204 2.21 5 O 6834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q GLU 42": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "X GLU 143": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z GLU 49": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a GLU 155": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 123": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "h GLU 39": "OE1" <-> "OE2" Residue "h GLU 59": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "l GLU 445": "OE1" <-> "OE2" Residue "m GLU 138": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 54": "OE1" <-> "OE2" Residue "o TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 134": "OE1" <-> "OE2" Residue "p GLU 176": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "r GLU 335": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "w GLU 47": "OE1" <-> "OE2" Residue "w GLU 160": "OE1" <-> "OE2" Residue "w GLU 189": "OE1" <-> "OE2" Residue "w GLU 197": "OE1" <-> "OE2" Residue "w GLU 213": "OE1" <-> "OE2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w GLU 267": "OE1" <-> "OE2" Residue "w GLU 333": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38846 Number of models: 1 Model: "" Number of chains: 43 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: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1015 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 945 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} 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: "X" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 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: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1012 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "w" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2583 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 134 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 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: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 149 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 245 Unusual residues: {'CDL': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "o" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 68 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "r" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "s" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {' UQ': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 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: "u" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 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: 19.50, per 1000 atoms: 0.50 Number of scatterers: 38846 At special positions: 0 Unit cell: (190.133, 184.762, 141.794, 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 31 15.00 O 6834 8.00 N 6204 7.00 C 25492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=1.55 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.51 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=1.64 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.03 Conformation dependent library (CDL) restraints added in 6.5 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: 204 helices and 4 sheets defined 63.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.068A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 60 removed outlier: 4.323A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 57 through 60' Processing helix chain 'S' and resid 2 through 29 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 43 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'U' and resid 3 through 13 Processing helix chain 'U' and resid 17 through 34 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'V' and resid 4 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 33 through 98 Proline residue: W 73 - end of helix 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: 6.282A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.606A 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: 4.544A 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 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 29 through 37 Processing helix chain 'Z' and resid 46 through 53 removed outlier: 3.651A pdb=" N GLU Z 49 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 58 No H-bonds generated for 'chain 'Z' and resid 56 through 58' 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 removed outlier: 3.547A pdb=" N THR a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 4.026A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 65 through 73 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 126 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.664A 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 121 through 124 No H-bonds generated for 'chain 'd' and resid 121 through 124' Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 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 No H-bonds generated for '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: 3.587A 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 94 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.386A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.836A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.809A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 191 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 4.022A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.421A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 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: 5.833A 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: 3.847A 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 23 removed outlier: 4.268A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.855A 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: 4.294A 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: 3.796A 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 157 removed outlier: 3.559A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP l 157 " --> pdb=" O LEU l 153 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 192 removed outlier: 3.948A 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: 4.193A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 250 removed outlier: 3.764A pdb=" N HIS l 248 " --> pdb=" O SER l 244 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER l 249 " --> pdb=" O ALA l 245 " (cutoff:3.500A) removed outlier: 3.974A 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 271 through 294 removed outlier: 4.567A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 3.726A 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: 4.766A 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: 3.723A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.046A 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: 3.803A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.833A 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 534 Proline residue: l 530 - end of helix removed outlier: 4.344A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 removed outlier: 3.882A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.259A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 8 through 34 removed outlier: 6.422A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.628A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 23 Processing helix chain 'o' and resid 27 through 51 Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 49 Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 66 through 73 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: 3.773A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.934A 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: 4.197A 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: 4.278A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 3.867A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.475A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.654A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.552A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.550A 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: 4.009A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 4.476A 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 204 removed outlier: 4.211A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.060A 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 249 removed outlier: 4.779A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 266 removed outlier: 4.664A pdb=" N TYR r 259 " --> pdb=" O ASN r 255 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 3.537A pdb=" N LEU r 264 " --> pdb=" O PRO r 260 " (cutoff:3.500A) Processing helix chain 'r' and resid 268 through 277 removed outlier: 3.564A 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: 3.653A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 392 through 415 removed outlier: 3.710A 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: 4.381A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 453 No H-bonds generated for 'chain 'r' and resid 451 through 453' Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.639A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 88 Proline residue: s 75 - end of helix removed outlier: 4.269A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL s 87 " --> pdb=" O LEU s 83 " (cutoff:3.500A) Proline residue: s 88 - end of helix Processing helix chain 's' and resid 101 through 123 removed outlier: 4.246A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.880A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.654A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 177 No H-bonds generated for 'chain 's' and resid 174 through 177' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 218 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 311 removed outlier: 5.073A 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 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 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 19 through 21 No H-bonds generated for 'chain 'v' and resid 19 through 21' Processing helix chain 'v' and resid 27 through 29 No H-bonds generated for 'chain 'v' and resid 27 through 29' Processing helix chain 'v' and resid 43 through 48 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 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: 5.054A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 251 removed outlier: 3.770A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 275 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.181A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 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: 6.423A 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: 6.709A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'w' and resid 84 through 86 1999 hydrogen bonds defined for protein. 5700 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: 13.15 Time building geometry restraints manager: 17.21 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: 5885 1.31 - 1.43: 10769 1.43 - 1.56: 22533 1.56 - 1.69: 144 1.69 - 1.82: 516 Bond restraints: 39847 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C18 UQ s 403 " pdb=" C19 UQ s 403 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CA7 CDL i 401 " pdb=" OA8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CA7 CDL o 201 " pdb=" OA8 CDL o 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CA7 CDL a 201 " pdb=" OA8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 ... (remaining 39842 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.51: 1121 105.51 - 112.87: 21710 112.87 - 120.23: 15083 120.23 - 127.59: 15381 127.59 - 134.96: 522 Bond angle restraints: 53817 Sorted by residual: angle pdb=" N GLY a 94 " pdb=" CA GLY a 94 " pdb=" C GLY a 94 " ideal model delta sigma weight residual 111.36 123.28 -11.92 1.17e+00 7.31e-01 1.04e+02 angle pdb=" N PHE a 92 " pdb=" CA PHE a 92 " pdb=" C PHE a 92 " ideal model delta sigma weight residual 111.36 120.80 -9.44 1.09e+00 8.42e-01 7.49e+01 angle pdb=" C TYR c 75 " pdb=" N PRO c 76 " pdb=" CA PRO c 76 " ideal model delta sigma weight residual 119.85 128.19 -8.34 1.01e+00 9.80e-01 6.82e+01 angle pdb=" C VAL s 87 " pdb=" N PRO s 88 " pdb=" CA PRO s 88 " ideal model delta sigma weight residual 118.85 127.65 -8.80 1.09e+00 8.42e-01 6.52e+01 angle pdb=" C11 CDL l 701 " pdb=" CA5 CDL l 701 " pdb=" OA6 CDL l 701 " ideal model delta sigma weight residual 111.33 121.99 -10.66 1.32e+00 5.72e-01 6.50e+01 ... (remaining 53812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 23309 35.92 - 71.83: 793 71.83 - 107.75: 55 107.75 - 143.66: 23 143.66 - 179.58: 8 Dihedral angle restraints: 24188 sinusoidal: 10550 harmonic: 13638 Sorted by residual: dihedral pdb=" CB CYS V 95 " pdb=" SG CYS V 95 " pdb=" SG CYS V 115 " pdb=" CB CYS V 115 " ideal model delta sinusoidal sigma weight residual -86.00 -26.46 -59.54 1 1.00e+01 1.00e-02 4.73e+01 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 98.97 -158.97 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" CB CYS u 88 " pdb=" SG CYS u 88 " pdb=" SG CYS u 100 " pdb=" CB CYS u 100 " ideal model delta sinusoidal sigma weight residual -86.00 -140.49 54.49 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 24185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 5480 0.092 - 0.185: 327 0.185 - 0.277: 24 0.277 - 0.370: 5 0.370 - 0.462: 2 Chirality restraints: 5838 Sorted by residual: chirality pdb=" CA PHE a 92 " pdb=" N PHE a 92 " pdb=" C PHE a 92 " pdb=" CB PHE a 92 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA TRP u 86 " pdb=" N TRP u 86 " pdb=" C TRP u 86 " pdb=" CB TRP u 86 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CA HIS b 74 " pdb=" N HIS b 74 " pdb=" C HIS b 74 " pdb=" CB HIS b 74 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 5835 not shown) Planarity restraints: 6574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 403 " -0.345 2.00e-02 2.50e+03 4.91e-01 3.01e+03 pdb=" C11 UQ s 403 " -0.225 2.00e-02 2.50e+03 pdb=" C7 UQ s 403 " -0.578 2.00e-02 2.50e+03 pdb=" C8 UQ s 403 " 0.716 2.00e-02 2.50e+03 pdb=" C9 UQ s 403 " 0.432 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 403 " -0.246 2.00e-02 2.50e+03 2.52e-01 7.96e+02 pdb=" C18 UQ s 403 " 0.202 2.00e-02 2.50e+03 pdb=" C19 UQ s 403 " 0.359 2.00e-02 2.50e+03 pdb=" C20 UQ s 403 " -0.020 2.00e-02 2.50e+03 pdb=" C21 UQ s 403 " -0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 403 " 0.167 2.00e-02 2.50e+03 2.08e-01 5.38e+02 pdb=" C13 UQ s 403 " -0.100 2.00e-02 2.50e+03 pdb=" C14 UQ s 403 " -0.346 2.00e-02 2.50e+03 pdb=" C15 UQ s 403 " 0.045 2.00e-02 2.50e+03 pdb=" C16 UQ s 403 " 0.235 2.00e-02 2.50e+03 ... (remaining 6571 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 338 2.62 - 3.19: 34897 3.19 - 3.76: 61130 3.76 - 4.33: 87167 4.33 - 4.90: 143273 Nonbonded interactions: 326805 Sorted by model distance: nonbonded pdb=" OH TYR c 75 " pdb=" O ILE c 105 " model vdw 2.053 2.440 nonbonded pdb=" O27 8Q1 X 201 " pdb=" O33 8Q1 X 201 " model vdw 2.054 2.440 nonbonded pdb=" N PEE b 201 " pdb=" O2P PEE b 201 " model vdw 2.210 2.520 nonbonded pdb=" O LEU l 290 " pdb=" OG SER l 523 " model vdw 2.221 2.440 nonbonded pdb=" O MET r 14 " pdb=" OG SER r 18 " model vdw 2.223 2.440 ... (remaining 326800 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.110 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 97.630 Find NCS groups from input model: 1.200 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.226 39847 Z= 0.471 Angle : 0.912 17.355 53817 Z= 0.494 Chirality : 0.048 0.462 5838 Planarity : 0.009 0.491 6574 Dihedral : 17.857 179.580 15353 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 0.27 % Allowed : 0.76 % Favored : 98.97 % Cbeta Deviations : 0.05 % 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: 1.26 (0.13), residues: 4586 helix: 1.62 (0.10), residues: 2935 sheet: 0.45 (1.14), residues: 25 loop : -0.58 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP w 353 HIS 0.006 0.001 HIS r 30 PHE 0.033 0.002 PHE i 292 TYR 0.038 0.002 TYR s 277 ARG 0.008 0.000 ARG e 88 *********************** 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 927 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 916 time to evaluate : 4.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 79 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6823 (mm-30) REVERT: V 35 ILE cc_start: 0.8309 (mt) cc_final: 0.8103 (mt) REVERT: V 124 LEU cc_start: 0.9244 (mt) cc_final: 0.9037 (mp) REVERT: X 146 ASP cc_start: 0.7348 (m-30) cc_final: 0.6859 (m-30) REVERT: X 150 ASP cc_start: 0.7843 (m-30) cc_final: 0.7574 (m-30) REVERT: Z 43 ASP cc_start: 0.7339 (p0) cc_final: 0.7081 (p0) REVERT: Z 72 LYS cc_start: 0.8040 (mptt) cc_final: 0.7832 (mptt) REVERT: Z 73 TRP cc_start: 0.6199 (m-10) cc_final: 0.5899 (t60) REVERT: b 24 LYS cc_start: 0.9081 (tptp) cc_final: 0.8783 (tptp) REVERT: b 93 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8250 (mtpt) REVERT: c 70 MET cc_start: 0.7783 (mmt) cc_final: 0.7537 (mmt) REVERT: c 110 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8650 (p0) REVERT: d 6 ASP cc_start: 0.8880 (t70) cc_final: 0.8608 (t0) REVERT: e 124 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7472 (mtt180) REVERT: f 63 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8416 (mtpp) REVERT: f 68 GLU cc_start: 0.8714 (tp30) cc_final: 0.8437 (tp30) REVERT: h 80 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7567 (mtmt) REVERT: h 97 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.6580 (m90) REVERT: j 7 LEU cc_start: 0.9465 (mt) cc_final: 0.9252 (mt) REVERT: j 90 MET cc_start: 0.9006 (mmp) cc_final: 0.8463 (mmp) REVERT: k 9 ILE cc_start: 0.9297 (mm) cc_final: 0.8960 (mm) REVERT: k 43 MET cc_start: 0.8604 (tpt) cc_final: 0.8110 (tpt) REVERT: l 20 MET cc_start: 0.8412 (mtt) cc_final: 0.8156 (mtt) REVERT: l 53 MET cc_start: 0.8987 (mtm) cc_final: 0.8715 (mtp) REVERT: l 62 ILE cc_start: 0.8943 (mm) cc_final: 0.8714 (pt) REVERT: l 268 GLU cc_start: 0.8629 (pt0) cc_final: 0.8420 (pt0) REVERT: l 397 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7775 (mt-10) REVERT: l 525 MET cc_start: 0.8136 (mmm) cc_final: 0.7812 (mmm) REVERT: l 550 SER cc_start: 0.9009 (t) cc_final: 0.8649 (m) REVERT: m 3 MET cc_start: 0.5123 (mpp) cc_final: 0.4156 (mmt) REVERT: o 5 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7808 (tttm) REVERT: o 95 ILE cc_start: 0.9135 (mm) cc_final: 0.8859 (mt) REVERT: p 55 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7295 (mmtt) REVERT: p 65 ARG cc_start: 0.7774 (ttt-90) cc_final: 0.7492 (ttt-90) REVERT: p 159 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8348 (mttp) REVERT: r 180 HIS cc_start: 0.8625 (t-90) cc_final: 0.8377 (t-170) REVERT: s 70 MET cc_start: 0.7558 (mtt) cc_final: 0.7311 (mtt) REVERT: u 16 GLN cc_start: 0.7782 (tt0) cc_final: 0.7302 (tm-30) REVERT: v 22 MET cc_start: 0.8400 (mtt) cc_final: 0.7801 (ttm) REVERT: v 34 ARG cc_start: 0.6068 (ttt-90) cc_final: 0.2694 (mtp85) REVERT: v 54 GLN cc_start: 0.8667 (pt0) cc_final: 0.8385 (pm20) REVERT: w 221 LYS cc_start: 0.7542 (mtpt) cc_final: 0.6908 (mttp) REVERT: w 246 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8535 (mt) REVERT: w 303 GLU cc_start: 0.7328 (tt0) cc_final: 0.7122 (tp30) outliers start: 11 outliers final: 5 residues processed: 923 average time/residue: 0.5497 time to fit residues: 816.6120 Evaluate side-chains 743 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 735 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain c residue 110 ASP Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain w residue 246 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 0.8980 chunk 343 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 355 optimal weight: 2.9990 chunk 137 optimal weight: 0.0870 chunk 215 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 411 optimal weight: 4.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN S 44 GLN V 129 GLN Y 83 HIS Z 21 GLN d 134 GLN d 149 HIS i 49 ASN i 319 HIS j 10 ASN l 25 ASN l 400 ASN l 580 GLN r 192 ASN s 157 ASN s 194 ASN s 230 ASN s 235 ASN v 85 HIS w 235 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39847 Z= 0.181 Angle : 0.555 8.587 53817 Z= 0.277 Chirality : 0.040 0.178 5838 Planarity : 0.005 0.081 6574 Dihedral : 16.645 170.452 6231 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 1.01 % Allowed : 6.34 % Favored : 92.65 % 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: 1.60 (0.13), residues: 4586 helix: 1.91 (0.10), residues: 2938 sheet: 0.58 (1.14), residues: 25 loop : -0.50 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS Y 83 PHE 0.029 0.001 PHE i 292 TYR 0.025 0.001 TYR l 422 ARG 0.007 0.000 ARG d 60 *********************** 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 805 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 764 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 79 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6611 (mm-30) REVERT: W 85 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: X 146 ASP cc_start: 0.7498 (m-30) cc_final: 0.6920 (m-30) REVERT: X 150 ASP cc_start: 0.7860 (m-30) cc_final: 0.7570 (m-30) REVERT: Y 102 ASP cc_start: 0.5352 (t0) cc_final: 0.5074 (t0) REVERT: Z 72 LYS cc_start: 0.8082 (mptt) cc_final: 0.7839 (mptt) REVERT: Z 73 TRP cc_start: 0.6219 (m-10) cc_final: 0.5877 (t60) REVERT: a 160 MET cc_start: 0.9166 (mtt) cc_final: 0.8722 (mtt) REVERT: a 185 THR cc_start: 0.8094 (p) cc_final: 0.7874 (p) REVERT: b 24 LYS cc_start: 0.9143 (tptp) cc_final: 0.8851 (tptp) REVERT: b 93 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8164 (mtpt) REVERT: d 6 ASP cc_start: 0.8856 (t70) cc_final: 0.8646 (t0) REVERT: d 62 TYR cc_start: 0.8268 (m-10) cc_final: 0.8016 (m-80) REVERT: e 124 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7404 (mtt180) REVERT: e 125 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8899 (mt) REVERT: f 63 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8453 (mtpp) REVERT: h 13 ASP cc_start: 0.8657 (t0) cc_final: 0.8356 (t0) REVERT: h 80 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7583 (mtmt) REVERT: k 9 ILE cc_start: 0.9212 (mm) cc_final: 0.8846 (mm) REVERT: k 43 MET cc_start: 0.8554 (tpt) cc_final: 0.7893 (tpt) REVERT: l 20 MET cc_start: 0.8383 (mtt) cc_final: 0.8172 (mtt) REVERT: l 53 MET cc_start: 0.8967 (mtm) cc_final: 0.8699 (mtp) REVERT: l 62 ILE cc_start: 0.9036 (mm) cc_final: 0.8814 (pt) REVERT: l 482 MET cc_start: 0.8094 (mtp) cc_final: 0.7837 (mtp) REVERT: l 550 SER cc_start: 0.8936 (t) cc_final: 0.8629 (m) REVERT: l 573 MET cc_start: 0.8703 (mmm) cc_final: 0.8441 (mmp) REVERT: m 3 MET cc_start: 0.5015 (mpp) cc_final: 0.4174 (mmt) REVERT: m 169 MET cc_start: 0.8621 (mmm) cc_final: 0.7976 (mmm) REVERT: o 95 ILE cc_start: 0.9093 (mm) cc_final: 0.8689 (mm) REVERT: p 43 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8260 (mp) REVERT: p 55 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7193 (mmtt) REVERT: p 59 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7860 (ttmt) REVERT: p 159 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8306 (mttp) REVERT: r 10 MET cc_start: 0.8677 (mmp) cc_final: 0.8378 (mmp) REVERT: r 180 HIS cc_start: 0.8623 (t-90) cc_final: 0.8415 (t-170) REVERT: s 3 MET cc_start: 0.8084 (tpp) cc_final: 0.7847 (mmm) REVERT: s 70 MET cc_start: 0.7492 (mtt) cc_final: 0.7281 (mtt) REVERT: u 16 GLN cc_start: 0.7744 (tt0) cc_final: 0.7394 (tm-30) REVERT: v 22 MET cc_start: 0.8245 (mtt) cc_final: 0.7818 (ttm) REVERT: v 34 ARG cc_start: 0.6177 (ttt-90) cc_final: 0.2852 (mtp85) REVERT: v 46 MET cc_start: 0.8239 (ttt) cc_final: 0.8012 (ttt) REVERT: v 54 GLN cc_start: 0.8622 (pt0) cc_final: 0.8331 (pm20) REVERT: w 221 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7105 (mttp) outliers start: 41 outliers final: 28 residues processed: 786 average time/residue: 0.5259 time to fit residues: 674.2909 Evaluate side-chains 755 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 724 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 409 LEU Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain w residue 152 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 342 optimal weight: 0.3980 chunk 280 optimal weight: 10.0000 chunk 113 optimal weight: 0.0030 chunk 412 optimal weight: 0.9980 chunk 445 optimal weight: 8.9990 chunk 367 optimal weight: 1.9990 chunk 408 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 44 GLN S 68 ASN V 129 GLN a 189 ASN d 134 GLN j 10 ASN l 139 GLN l 580 GLN s 194 ASN s 235 ASN u 65 GLN w 127 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39847 Z= 0.213 Angle : 0.549 8.590 53817 Z= 0.275 Chirality : 0.040 0.217 5838 Planarity : 0.004 0.070 6574 Dihedral : 15.627 179.764 6222 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 1.60 % Allowed : 8.41 % Favored : 90.00 % 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: 1.67 (0.13), residues: 4586 helix: 1.96 (0.10), residues: 2944 sheet: 0.63 (1.15), residues: 25 loop : -0.48 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.009 0.001 HIS Y 83 PHE 0.031 0.001 PHE i 292 TYR 0.025 0.001 TYR W 138 ARG 0.006 0.000 ARG d 60 *********************** 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 811 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 746 time to evaluate : 4.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 28 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7932 (mmmt) REVERT: X 150 ASP cc_start: 0.7878 (m-30) cc_final: 0.7586 (m-30) REVERT: Y 102 ASP cc_start: 0.5179 (t0) cc_final: 0.4966 (t0) REVERT: Z 43 ASP cc_start: 0.7459 (p0) cc_final: 0.7227 (p0) REVERT: Z 72 LYS cc_start: 0.8147 (mptt) cc_final: 0.7873 (mptt) REVERT: Z 73 TRP cc_start: 0.6302 (m-10) cc_final: 0.5873 (t60) REVERT: a 185 THR cc_start: 0.8468 (p) cc_final: 0.8242 (p) REVERT: b 93 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8133 (mtpt) REVERT: d 62 TYR cc_start: 0.8277 (m-10) cc_final: 0.8066 (m-80) REVERT: e 124 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7454 (mtt180) REVERT: f 63 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8439 (mtpp) REVERT: h 13 ASP cc_start: 0.8587 (t0) cc_final: 0.8348 (t0) REVERT: k 9 ILE cc_start: 0.9221 (mm) cc_final: 0.8853 (mm) REVERT: l 20 MET cc_start: 0.8445 (mtt) cc_final: 0.8161 (mtt) REVERT: l 320 ASN cc_start: 0.8773 (t0) cc_final: 0.8506 (t0) REVERT: l 544 MET cc_start: 0.8179 (mmt) cc_final: 0.7904 (mmp) REVERT: l 550 SER cc_start: 0.8982 (t) cc_final: 0.8638 (m) REVERT: l 573 MET cc_start: 0.8749 (mmm) cc_final: 0.8519 (mmm) REVERT: m 1 MET cc_start: 0.4052 (OUTLIER) cc_final: 0.2471 (mmm) REVERT: m 3 MET cc_start: 0.5023 (mpp) cc_final: 0.4226 (mmt) REVERT: m 169 MET cc_start: 0.8671 (mmm) cc_final: 0.8103 (mtp) REVERT: o 95 ILE cc_start: 0.9074 (mm) cc_final: 0.8678 (mm) REVERT: p 43 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8305 (mp) REVERT: p 55 LYS cc_start: 0.7479 (mmtt) cc_final: 0.7275 (mmtt) REVERT: p 59 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7897 (ttmt) REVERT: r 10 MET cc_start: 0.8697 (mmp) cc_final: 0.8371 (mmp) REVERT: r 180 HIS cc_start: 0.8615 (t-90) cc_final: 0.8375 (t70) REVERT: r 302 MET cc_start: 0.8703 (mmp) cc_final: 0.8243 (mmt) REVERT: s 70 MET cc_start: 0.7509 (mtt) cc_final: 0.7275 (mtt) REVERT: v 21 ARG cc_start: 0.8134 (mmt180) cc_final: 0.7857 (mmt180) REVERT: v 22 MET cc_start: 0.8147 (mtt) cc_final: 0.7717 (ttm) REVERT: v 34 ARG cc_start: 0.6285 (ttt-90) cc_final: 0.3441 (mtp85) REVERT: v 46 MET cc_start: 0.8540 (ttt) cc_final: 0.8111 (ttp) REVERT: v 54 GLN cc_start: 0.8636 (pt0) cc_final: 0.8291 (pm20) REVERT: w 221 LYS cc_start: 0.7785 (mtpt) cc_final: 0.6766 (mttp) outliers start: 65 outliers final: 47 residues processed: 772 average time/residue: 0.5116 time to fit residues: 652.6786 Evaluate side-chains 771 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 722 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 40 SER Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain Z residue 20 LYS Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 42 ARG Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 576 MET Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 36 SER Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain r residue 350 THR Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 22 SER Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain v residue 65 GLN Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 152 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 196 optimal weight: 0.0870 chunk 276 optimal weight: 5.9990 chunk 413 optimal weight: 0.9990 chunk 437 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 chunk 391 optimal weight: 2.9990 chunk 118 optimal weight: 0.0770 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: