Starting phenix.real_space_refine on Tue Apr 16 10:53:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy1_32191/04_2024/7vy1_32191_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy1_32191/04_2024/7vy1_32191.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy1_32191/04_2024/7vy1_32191_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy1_32191/04_2024/7vy1_32191_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy1_32191/04_2024/7vy1_32191_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy1_32191/04_2024/7vy1_32191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy1_32191/04_2024/7vy1_32191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy1_32191/04_2024/7vy1_32191_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy1_32191/04_2024/7vy1_32191_updated.pdb" } resolution = 3.3 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= 0.003 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 32 5.49 5 S 286 5.16 5 C 25535 2.51 5 N 6213 2.21 5 O 6833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q GLU 45": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 95": "OE1" <-> "OE2" Residue "Z GLU 15": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d GLU 128": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "g GLU 105": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h GLU 89": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "j GLU 68": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 238": "OE1" <-> "OE2" Residue "l GLU 353": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p GLU 101": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "s PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 84": "OE1" <-> "OE2" Residue "v GLU 33": "OE1" <-> "OE2" Residue "v GLU 101": "OE1" <-> "OE2" Residue "v GLU 105": "OE1" <-> "OE2" Residue "w GLU 171": "OE1" <-> "OE2" Residue "w GLU 197": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38899 Number of models: 1 Model: "" Number of chains: 44 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: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 597 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 875 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 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: "c" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1299 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 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: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2581 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 94 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 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: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 147 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 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: 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: "l" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 186 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 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: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 254 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "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=0.59 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.59 Time building chain proxies: 19.13, per 1000 atoms: 0.49 Number of scatterers: 38899 At special positions: 0 Unit cell: (181.54, 191.208, 139.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 286 16.00 P 32 15.00 O 6833 8.00 N 6213 7.00 C 25535 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=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.74 Conformation dependent library (CDL) restraints added in 7.3 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: 196 helices and 4 sheets defined 62.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.52 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 48 removed outlier: 4.153A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 60 removed outlier: 4.257A 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 31 Proline residue: S 7 - end of helix removed outlier: 4.491A pdb=" N ILE S 18 " --> pdb=" O CYS S 15 " (cutoff:3.500A) Proline residue: S 19 - end of helix removed outlier: 4.439A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 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 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 removed outlier: 3.677A 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: 3.814A 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: 6.018A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.955A 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 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' 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 39 removed outlier: 3.671A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 53 removed outlier: 4.800A 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 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 26 Processing helix chain 'b' and resid 65 through 73 removed outlier: 3.520A pdb=" N VAL b 72 " --> pdb=" O SER b 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 59 through 61 No H-bonds generated for 'chain 'c' and resid 59 through 61' 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: 4.337A 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 82 through 116 Processing helix chain 'd' and resid 118 through 124 removed outlier: 3.613A pdb=" N TYR d 121 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG d 122 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 3.773A 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 80 through 94 Processing helix chain 'e' and resid 98 through 107 removed outlier: 3.915A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 131 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 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 43 Processing helix chain 'h' and resid 49 through 55 Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain '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: 3.580A 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: 4.277A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 132 Processing helix chain 'i' and resid 134 through 145 removed outlier: 3.812A pdb=" N ALA i 137 " --> pdb=" O GLN i 134 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.872A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 193 removed outlier: 3.598A pdb=" N ALA i 192 " --> pdb=" O GLY i 188 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.902A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.513A 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: 4.337A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 315 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 345 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 26 Proline residue: j 25 - end of helix Processing helix chain 'j' and resid 53 through 78 Proline residue: j 74 - end of helix removed outlier: 5.851A 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: 3.899A 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: 4.224A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.754A 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: 4.618A 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: 3.869A 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: 3.503A pdb=" N GLY l 148 " --> pdb=" O TRP l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.943A 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: 4.364A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 267 No H-bonds generated for 'chain 'l' and resid 264 through 267' Processing helix chain 'l' and resid 272 through 294 removed outlier: 4.253A 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: 3.690A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 387 through 400 removed outlier: 4.044A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.580A 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 470 removed outlier: 3.594A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.253A 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: 3.605A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.801A 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: 4.218A 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: 4.073A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.291A 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 15 through 34 removed outlier: 3.800A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (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 62 Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 3.778A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.793A 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: 4.091A 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: 4.299A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 removed outlier: 3.883A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.850A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.643A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 142 through 171 removed outlier: 3.569A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.788A pdb=" N VAL r 162 " --> pdb=" O LEU r 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.021A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.152A 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: 5.040A 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: 4.341A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.668A 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: 3.643A 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: 3.548A 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: 4.341A 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 31 Proline residue: s 12 - end of helix removed outlier: 4.030A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.395A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 4.374A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 3.854A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.738A 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 275 Processing helix chain 's' and resid 282 through 311 removed outlier: 4.978A 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 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 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 No H-bonds generated for '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 166 through 176 removed outlier: 3.655A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN w 176 " --> pdb=" O MET w 173 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 5.069A 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 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: 3.971A 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: 3.615A pdb=" N ASN l 65 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.545A 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: 6.632A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.676A 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 1995 hydrogen bonds defined for protein. 5712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.33 Time building geometry restraints manager: 17.00 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: 5874 1.31 - 1.44: 10823 1.44 - 1.56: 22522 1.56 - 1.69: 164 1.69 - 1.82: 517 Bond restraints: 39900 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=" C4' ADP w 401 " pdb=" O4' ADP w 401 " ideal model delta sigma weight residual 1.426 1.617 -0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" CA7 CDL u 201 " pdb=" OA8 CDL u 201 " ideal model delta sigma weight residual 1.334 1.430 -0.096 1.10e-02 8.26e+03 7.68e+01 bond pdb=" CA7 CDL V 201 " pdb=" OA8 CDL V 201 " ideal model delta sigma weight residual 1.334 1.430 -0.096 1.10e-02 8.26e+03 7.56e+01 bond pdb=" CA7 CDL i 401 " pdb=" OA8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.429 -0.095 1.10e-02 8.26e+03 7.50e+01 ... (remaining 39895 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.29: 1079 105.29 - 112.57: 21126 112.57 - 119.85: 13654 119.85 - 127.13: 17406 127.13 - 134.41: 613 Bond angle restraints: 53878 Sorted by residual: angle pdb=" C ASP e 143 " pdb=" N PRO e 144 " pdb=" CA PRO e 144 " ideal model delta sigma weight residual 119.05 127.31 -8.26 1.11e+00 8.12e-01 5.54e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.78 -9.45 1.32e+00 5.72e-01 5.11e+01 angle pdb=" C51 CDL r 504 " pdb=" CB5 CDL r 504 " pdb=" OB6 CDL r 504 " ideal model delta sigma weight residual 111.33 120.59 -9.26 1.32e+00 5.72e-01 4.91e+01 angle pdb=" C51 CDL u 201 " pdb=" CB5 CDL u 201 " pdb=" OB6 CDL u 201 " ideal model delta sigma weight residual 111.33 120.43 -9.10 1.32e+00 5.72e-01 4.74e+01 angle pdb=" C11 CDL i 401 " pdb=" CA5 CDL i 401 " pdb=" OA6 CDL i 401 " ideal model delta sigma weight residual 111.33 120.38 -9.05 1.32e+00 5.72e-01 4.69e+01 ... (remaining 53873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 23107 35.10 - 70.20: 1023 70.20 - 105.30: 73 105.30 - 140.40: 18 140.40 - 175.50: 5 Dihedral angle restraints: 24226 sinusoidal: 10588 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 300.00 124.50 175.50 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C32 PEE W 201 " pdb=" C30 PEE W 201 " pdb=" C31 PEE W 201 " pdb=" O3 PEE W 201 " ideal model delta sinusoidal sigma weight residual 161.16 -2.62 163.78 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CA5 CDL V 201 " pdb=" CA4 CDL V 201 " pdb=" OA6 CDL V 201 " pdb=" CA6 CDL V 201 " ideal model delta sinusoidal sigma weight residual 168.24 -37.97 -153.79 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 24223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5049 0.061 - 0.122: 745 0.122 - 0.183: 40 0.183 - 0.243: 7 0.243 - 0.304: 1 Chirality restraints: 5842 Sorted by residual: chirality pdb=" CA TRP i 133 " pdb=" N TRP i 133 " pdb=" C TRP i 133 " pdb=" CB TRP i 133 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA CYS w 67 " pdb=" N CYS w 67 " pdb=" C CYS w 67 " pdb=" CB CYS w 67 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C2 PEE W 201 " pdb=" C1 PEE W 201 " pdb=" C3 PEE W 201 " pdb=" O2 PEE W 201 " both_signs ideal model delta sigma weight residual False -2.33 -2.55 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 5839 not shown) Planarity restraints: 6572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP v 18 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO v 19 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO v 19 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO v 19 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN l 320 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ASN l 320 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN l 320 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN l 321 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP d 38 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ASP d 38 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP d 38 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU d 39 " 0.013 2.00e-02 2.50e+03 ... (remaining 6569 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 417 2.63 - 3.20: 34730 3.20 - 3.76: 60482 3.76 - 4.33: 82978 4.33 - 4.90: 140346 Nonbonded interactions: 318953 Sorted by model distance: nonbonded pdb=" OE2 GLU e 151 " pdb=" OD1 ASP e 152 " model vdw 2.061 3.040 nonbonded pdb=" O ARG w 261 " pdb=" NH1 ARG w 261 " model vdw 2.165 2.520 nonbonded pdb=" OG SER w 123 " pdb=" OD1 ASP w 125 " model vdw 2.212 2.440 nonbonded pdb=" OE1 GLU p 101 " pdb=" NH1 ARG p 122 " model vdw 2.216 2.520 nonbonded pdb=" OH TYR a 133 " pdb=" OE1 GLU d 87 " model vdw 2.218 2.440 ... (remaining 318948 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=0.59 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: 2.310 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: 9.680 Check model and map are aligned: 0.600 Set scattering table: 0.340 Process input model: 98.410 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.130 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 39900 Z= 0.466 Angle : 0.818 17.326 53878 Z= 0.415 Chirality : 0.042 0.304 5842 Planarity : 0.004 0.071 6572 Dihedral : 18.704 175.498 15394 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 0.20 % Allowed : 13.15 % Favored : 86.66 % 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: 1.76 (0.13), residues: 4586 helix: 2.09 (0.10), residues: 2953 sheet: 0.92 (1.10), residues: 24 loop : -0.58 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS v 61 PHE 0.030 0.001 PHE i 292 TYR 0.030 0.001 TYR w 129 ARG 0.008 0.000 ARG n 30 *********************** 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 722 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 714 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 130 ASN cc_start: 0.8420 (m-40) cc_final: 0.8163 (t0) REVERT: a 78 THR cc_start: 0.8508 (m) cc_final: 0.8037 (m) REVERT: h 65 GLU cc_start: 0.8948 (tp30) cc_final: 0.8667 (tp30) REVERT: i 284 MET cc_start: 0.8961 (mmm) cc_final: 0.8619 (mmt) REVERT: o 117 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8040 (mp10) REVERT: r 1 MET cc_start: 0.8910 (ttm) cc_final: 0.8695 (ttt) REVERT: u 90 ASP cc_start: 0.9075 (t70) cc_final: 0.8721 (t0) REVERT: v 38 GLU cc_start: 0.8452 (pm20) cc_final: 0.8231 (pm20) outliers start: 8 outliers final: 5 residues processed: 717 average time/residue: 0.5258 time to fit residues: 616.7332 Evaluate side-chains 704 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 699 time to evaluate : 4.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain w residue 285 ASP 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: 0.7980 chunk 190 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 355 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 411 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 83 GLN d 124 ASN ** l 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 235 ASN v 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39900 Z= 0.190 Angle : 0.537 9.790 53878 Z= 0.263 Chirality : 0.039 0.171 5842 Planarity : 0.004 0.051 6572 Dihedral : 16.116 160.201 6264 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 1.43 % Allowed : 13.05 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.13), residues: 4586 helix: 2.18 (0.10), residues: 2960 sheet: 1.13 (1.12), residues: 24 loop : -0.56 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.004 0.001 HIS v 61 PHE 0.028 0.001 PHE i 292 TYR 0.024 0.001 TYR w 129 ARG 0.005 0.000 ARG n 30 *********************** 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 784 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 726 time to evaluate : 4.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 122 MET cc_start: 0.8645 (mmm) cc_final: 0.8410 (mmm) REVERT: Z 23 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8498 (mmtt) REVERT: a 78 THR cc_start: 0.8427 (m) cc_final: 0.7941 (m) REVERT: h 65 GLU cc_start: 0.8942 (tp30) cc_final: 0.8704 (tp30) REVERT: i 11 MET cc_start: 0.8382 (mmp) cc_final: 0.8060 (mmm) REVERT: i 284 MET cc_start: 0.8988 (mmm) cc_final: 0.8704 (mmt) REVERT: m 34 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8894 (mp) REVERT: m 170 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8238 (mm-30) REVERT: p 123 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8010 (mp0) REVERT: s 287 HIS cc_start: 0.8314 (m-70) cc_final: 0.7539 (t-90) REVERT: u 90 ASP cc_start: 0.9053 (t70) cc_final: 0.8626 (t0) REVERT: v 33 GLU cc_start: 0.7907 (pm20) cc_final: 0.7545 (pm20) REVERT: v 38 GLU cc_start: 0.8448 (pm20) cc_final: 0.8221 (pm20) REVERT: w 246 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8179 (mm) outliers start: 58 outliers final: 32 residues processed: 756 average time/residue: 0.5386 time to fit residues: 671.7032 Evaluate side-chains 732 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 698 time to evaluate : 4.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain W residue 103 ASP Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 90 SER Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Z residue 68 LEU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 97 GLN Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 34 ILE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 50 GLU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain w residue 246 LEU Chi-restraints excluded: chain w residue 277 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 342 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 445 optimal weight: 6.9990 chunk 367 optimal weight: 0.3980 chunk 408 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 330 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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: