Starting phenix.real_space_refine on Fri Feb 23 20:02:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxs_32187/02_2024/7vxs_32187_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxs_32187/02_2024/7vxs_32187.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxs_32187/02_2024/7vxs_32187_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxs_32187/02_2024/7vxs_32187_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxs_32187/02_2024/7vxs_32187_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxs_32187/02_2024/7vxs_32187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxs_32187/02_2024/7vxs_32187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxs_32187/02_2024/7vxs_32187_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxs_32187/02_2024/7vxs_32187_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 37 5.49 5 S 293 5.16 5 C 26074 2.51 5 N 6284 2.21 5 O 6986 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 "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "V GLU 131": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 15": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "b GLU 122": "OE1" <-> "OE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 103": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "d PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "e GLU 151": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "l GLU 145": "OE1" <-> "OE2" Residue "l GLU 207": "OE1" <-> "OE2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "n GLU 54": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p GLU 95": "OE1" <-> "OE2" Residue "r GLU 87": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 192": "OE1" <-> "OE2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u GLU 155": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 33": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 254": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39674 Number of models: 1 Model: "" Number of chains: 43 Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 7, 'TRANS': 36} Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 949 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 694 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4816 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 28, 'TRANS': 577} Chain: "m" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1291 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 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: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2590 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 115 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "j" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "l" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 290 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 203 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 181 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.67 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.67 Time building chain proxies: 20.44, per 1000 atoms: 0.52 Number of scatterers: 39674 At special positions: 0 Unit cell: (183.688, 190.133, 137.498, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 293 16.00 P 37 15.00 O 6986 8.00 N 6284 7.00 C 26074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=1.60 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.39 Conformation dependent library (CDL) restraints added in 6.9 seconds 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 4 sheets defined 62.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.44 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.304A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 60 removed outlier: 4.121A 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 removed outlier: 3.618A pdb=" N ILE S 5 " --> pdb=" O TRP S 2 " (cutoff:3.500A) Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'U' and resid 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 33 through 99 Proline residue: W 73 - end of helix removed outlier: 3.638A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 137 Processing helix chain 'W' and resid 139 through 142 No H-bonds generated for 'chain 'W' and resid 139 through 142' Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 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 28 through 39 removed outlier: 3.734A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 54 Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 25 Processing helix chain 'b' and resid 69 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 129 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 4.917A 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: 3.854A pdb=" N TYR d 121 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG d 122 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 3.928A 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 106 Processing helix chain 'e' and resid 116 through 132 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.791A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 53 removed outlier: 3.637A pdb=" N GLU h 53 " --> pdb=" O GLY h 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 49 through 53' Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 44 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: 4.253A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.945A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.951A 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 170 removed outlier: 3.660A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.683A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 252 Processing helix chain 'i' and resid 258 through 271 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.404A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 4.135A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.594A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 21 Processing helix chain 'k' and resid 27 through 50 Processing helix chain 'k' and resid 55 through 85 removed outlier: 3.802A 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: 3.791A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.959A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.467A 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: 3.894A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 132 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.883A 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: 4.092A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.081A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 272 through 294 removed outlier: 4.431A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.064A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 381 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.824A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.742A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 5.767A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.297A 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: 3.852A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 533 Proline residue: l 530 - end of helix removed outlier: 4.060A 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 577 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 27 through 46 Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.292A 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 4 through 34 removed outlier: 6.399A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.641A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 23 No H-bonds generated for 'chain 'o' and resid 20 through 23' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.712A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.316A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 73 Processing helix chain 'p' and resid 93 through 96 removed outlier: 4.338A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 93 through 96' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 142 removed outlier: 4.649A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.238A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 60 through 80 Proline residue: r 64 - end of helix Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 110 Processing helix chain 'r' and resid 115 through 135 removed outlier: 4.743A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.403A 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 170 removed outlier: 4.080A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.665A 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: 4.493A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.256A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 250 removed outlier: 5.069A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.816A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 283 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.523A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 392 through 415 removed outlier: 3.571A pdb=" N GLN r 415 " --> pdb=" O LEU r 411 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.727A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.424A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.844A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.107A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 168 Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 213 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 291 removed outlier: 3.972A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 293 through 311 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 13 Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 79 through 91 Processing helix chain 'u' and resid 102 through 114 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 124 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 94 through 96 No H-bonds generated for 'chain 'w' and resid 94 through 96' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 163 through 175 removed outlier: 3.571A pdb=" N ASP w 166 " --> pdb=" O ILE w 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE w 167 " --> pdb=" O TYR w 164 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL w 168 " --> pdb=" O SER w 165 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE w 169 " --> pdb=" O ASP w 166 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.254A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.717A 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 251 removed outlier: 5.098A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.886A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 263 No H-bonds generated for 'chain 'w' and resid 261 through 263' Processing helix chain 'w' and resid 266 through 274 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: 4.926A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= B, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.395A 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: 6.806A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.324A 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 2006 hydrogen bonds defined for protein. 5775 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: 16.02 Time building geometry restraints manager: 16.89 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: 5984 1.31 - 1.44: 10976 1.44 - 1.57: 23023 1.57 - 1.70: 171 1.70 - 1.82: 529 Bond restraints: 40683 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=" CB7 CDL i 401 " pdb=" OB8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+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 1.18e+02 bond pdb=" CA7 CDL n 102 " pdb=" OA8 CDL n 102 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CA7 CDL l 702 " pdb=" OA8 CDL l 702 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 ... (remaining 40678 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.69: 1205 105.69 - 112.81: 22028 112.81 - 119.94: 13964 119.94 - 127.07: 17070 127.07 - 134.19: 614 Bond angle restraints: 54881 Sorted by residual: angle pdb=" C ASP Z 43 " pdb=" N PRO Z 44 " pdb=" CA PRO Z 44 " ideal model delta sigma weight residual 118.85 131.71 -12.86 1.09e+00 8.42e-01 1.39e+02 angle pdb=" N ILE s 68 " pdb=" CA ILE s 68 " pdb=" C ILE s 68 " ideal model delta sigma weight residual 110.62 118.58 -7.96 1.02e+00 9.61e-01 6.08e+01 angle pdb=" C ARG s 62 " pdb=" N PRO s 63 " pdb=" CA PRO s 63 " ideal model delta sigma weight residual 119.78 127.72 -7.94 1.03e+00 9.43e-01 5.94e+01 angle pdb=" C11 CDL l 702 " pdb=" CA5 CDL l 702 " pdb=" OA6 CDL l 702 " ideal model delta sigma weight residual 111.33 121.25 -9.92 1.32e+00 5.72e-01 5.64e+01 angle pdb=" N MET b 120 " pdb=" CA MET b 120 " pdb=" C MET b 120 " ideal model delta sigma weight residual 109.39 121.19 -11.80 1.59e+00 3.96e-01 5.50e+01 ... (remaining 54876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 23391 34.04 - 68.08: 1285 68.08 - 102.12: 81 102.12 - 136.17: 19 136.17 - 170.21: 14 Dihedral angle restraints: 24790 sinusoidal: 10930 harmonic: 13860 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 96.24 -156.24 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" CA ARG c 114 " pdb=" C ARG c 114 " pdb=" N ASN c 115 " pdb=" CA ASN c 115 " ideal model delta harmonic sigma weight residual 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA SER m 25 " pdb=" C SER m 25 " pdb=" N PRO m 26 " pdb=" CA PRO m 26 " ideal model delta harmonic sigma weight residual 180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 24787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5533 0.079 - 0.158: 372 0.158 - 0.238: 22 0.238 - 0.317: 1 0.317 - 0.396: 3 Chirality restraints: 5931 Sorted by residual: chirality pdb=" CA MET b 120 " pdb=" N MET b 120 " pdb=" C MET b 120 " pdb=" CB MET b 120 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA LYS b 121 " pdb=" N LYS b 121 " pdb=" C LYS b 121 " pdb=" CB LYS b 121 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA THR a 185 " pdb=" N THR a 185 " pdb=" C THR a 185 " pdb=" CB THR a 185 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 5928 not shown) Planarity restraints: 6676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG n 50 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO n 51 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO n 51 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO n 51 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET r 401 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C MET r 401 " 0.035 2.00e-02 2.50e+03 pdb=" O MET r 401 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE r 402 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER r 407 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C SER r 407 " 0.035 2.00e-02 2.50e+03 pdb=" O SER r 407 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU r 408 " -0.012 2.00e-02 2.50e+03 ... (remaining 6673 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 440 2.64 - 3.20: 35319 3.20 - 3.77: 62049 3.77 - 4.33: 86453 4.33 - 4.90: 144434 Nonbonded interactions: 328695 Sorted by model distance: nonbonded pdb=" OE2 GLU Z 49 " pdb=" NE ARG p 34 " model vdw 2.074 2.520 nonbonded pdb=" OH TYR o 23 " pdb=" OE1 GLU p 68 " model vdw 2.103 2.440 nonbonded pdb=" OE2 GLU Z 49 " pdb=" NH2 ARG p 34 " model vdw 2.117 2.520 nonbonded pdb=" OD1 ASP a 188 " pdb=" NH2 ARG u 47 " model vdw 2.117 2.520 nonbonded pdb=" O ASP Y 76 " pdb=" OH TYR l 385 " model vdw 2.151 2.440 ... (remaining 328690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.67 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.970 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 101.600 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.170 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 40683 Z= 0.452 Angle : 0.825 17.298 54881 Z= 0.428 Chirality : 0.042 0.396 5931 Planarity : 0.004 0.075 6676 Dihedral : 19.416 170.208 15812 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 1.04 % Allowed : 15.39 % Favored : 83.57 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.13), residues: 4666 helix: 2.18 (0.10), residues: 2917 sheet: -0.41 (0.87), residues: 40 loop : -0.80 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS r 30 PHE 0.030 0.001 PHE i 292 TYR 0.019 0.001 TYR l 422 ARG 0.015 0.000 ARG w 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 677 time to evaluate : 4.502 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: a 58 LYS cc_start: 0.9019 (mtmp) cc_final: 0.8663 (mtpp) REVERT: g 27 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8207 (mttm) REVERT: o 111 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8279 (mtmt) REVERT: w 51 ARG cc_start: 0.8396 (ptp-170) cc_final: 0.8135 (mtm-85) REVERT: w 227 MET cc_start: 0.8524 (mpp) cc_final: 0.8169 (mpp) outliers start: 43 outliers final: 25 residues processed: 708 average time/residue: 1.6779 time to fit residues: 1422.7717 Evaluate side-chains 688 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 663 time to evaluate : 4.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 79 SER Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 343 SER Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 73 SER Chi-restraints excluded: chain p residue 4 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 31 SER Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 386 optimal weight: 4.9990 chunk 347 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 358 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 415 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN g 18 ASN h 21 GLN h 27 HIS i 319 HIS l 109 HIS l 135 ASN l 199 GLN l 580 GLN n 3 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40683 Z= 0.269 Angle : 0.562 8.886 54881 Z= 0.279 Chirality : 0.042 0.227 5931 Planarity : 0.005 0.056 6676 Dihedral : 17.595 161.220 6604 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 95.99 % Rotamer: Outliers : 2.69 % Allowed : 13.93 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.13), residues: 4666 helix: 2.09 (0.10), residues: 2927 sheet: -0.68 (0.84), residues: 40 loop : -0.78 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 PHE 0.033 0.001 PHE i 292 TYR 0.025 0.001 TYR l 587 ARG 0.008 0.000 ARG w 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 671 time to evaluate : 4.706 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 52 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7559 (mtp) REVERT: S 4 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8663 (mt-10) REVERT: U 62 ASN cc_start: 0.8161 (t0) cc_final: 0.7939 (t160) REVERT: W 98 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7244 (mpt) REVERT: Y 62 SER cc_start: 0.8812 (m) cc_final: 0.8597 (m) REVERT: Z 85 GLU cc_start: 0.5419 (tt0) cc_final: 0.4964 (tt0) REVERT: c 34 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8163 (mmmt) REVERT: g 27 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8217 (mttm) REVERT: g 113 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: l 111 ASP cc_start: 0.9248 (OUTLIER) cc_final: 0.8801 (t70) REVERT: m 81 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: o 111 LYS cc_start: 0.8696 (mtpp) cc_final: 0.8291 (mtmt) REVERT: s 62 ARG cc_start: 0.8170 (ptt90) cc_final: 0.7529 (ptt-90) REVERT: v 46 MET cc_start: 0.8742 (mtm) cc_final: 0.8478 (mtp) REVERT: w 75 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7460 (mtp85) REVERT: w 227 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8146 (mmt) outliers start: 111 outliers final: 54 residues processed: 713 average time/residue: 1.6188 time to fit residues: 1387.4855 Evaluate side-chains 706 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 645 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 170 GLU Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 297 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 231 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 346 optimal weight: 0.4980 chunk 283 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 416 optimal weight: 3.9990 chunk 450 optimal weight: 0.7980 chunk 371 optimal weight: 0.8980 chunk 413 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN a 189 ASN b 13 GLN e 148 GLN g 18 ASN h 21 GLN i 319 HIS l 109 HIS l 135 ASN l 199 GLN m 86 ASN n 3 ASN p 66 GLN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 40683 Z= 0.157 Angle : 0.504 7.816 54881 Z= 0.252 Chirality : 0.039 0.199 5931 Planarity : 0.004 0.051 6676 Dihedral : 16.532 173.133 6582 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 2.79 % Allowed : 14.83 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.13), residues: 4666 helix: 2.23 (0.10), residues: 2917 sheet: -0.74 (0.82), residues: 40 loop : -0.72 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 PHE 0.028 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.006 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 672 time to evaluate : 4.416 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 4 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: U 10 LYS cc_start: 0.7796 (tptt) cc_final: 0.6856 (tttt) REVERT: U 62 ASN cc_start: 0.8189 (t0) cc_final: 0.7941 (t160) REVERT: W 98 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7177 (mpt) REVERT: X 98 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8304 (pt) REVERT: Z 14 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5519 (pp-130) REVERT: Z 49 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: Z 85 GLU cc_start: 0.5432 (tt0) cc_final: 0.4963 (tt0) REVERT: c 34 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8200 (mmmt) REVERT: e 137 MET cc_start: 0.9074 (tpp) cc_final: 0.8839 (ttp) REVERT: g 27 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8219 (mttm) REVERT: g 113 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: h 65 GLU cc_start: 0.9093 (tp30) cc_final: 0.8839 (tm-30) REVERT: h 102 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7099 (pt0) REVERT: l 70 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8910 (m) REVERT: l 111 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8775 (t70) REVERT: m 139 GLU cc_start: 0.8605 (tt0) cc_final: 0.8296 (tt0) REVERT: o 111 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8298 (mtmt) REVERT: v 46 MET cc_start: 0.8814 (mtm) cc_final: 0.8565 (mtp) REVERT: v 53 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8627 (tp) REVERT: w 75 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7387 (mtp85) REVERT: w 223 ASN cc_start: 0.8359 (t0) cc_final: 0.7699 (t0) REVERT: w 227 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7742 (mpt) outliers start: 115 outliers final: 46 residues processed: 718 average time/residue: 1.6162 time to fit residues: 1397.1814 Evaluate side-chains 713 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 656 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 244 MET Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 76 ASN Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 297 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 411 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 198 optimal weight: 0.3980 chunk 279 optimal weight: 3.9990 chunk 418 optimal weight: 2.9990 chunk 442 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 396 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN a 189 ASN b 13 GLN g 18 ASN h 21 GLN i 319 HIS l 109 HIS l 135 ASN l 199 GLN m 86 ASN n 3 ASN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40683 Z= 0.215 Angle : 0.526 7.930 54881 Z= 0.263 Chirality : 0.040 0.223 5931 Planarity : 0.004 0.053 6676 Dihedral : 15.707 175.595 6581 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 3.28 % Allowed : 14.83 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.13), residues: 4666 helix: 2.19 (0.10), residues: 2920 sheet: -0.76 (0.82), residues: 40 loop : -0.70 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 PHE 0.031 0.001 PHE i 292 TYR 0.023 0.001 TYR l 587 ARG 0.008 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 661 time to evaluate : 4.886 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 4 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8582 (mt-10) REVERT: U 62 ASN cc_start: 0.8234 (t0) cc_final: 0.7964 (t160) REVERT: W 98 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7145 (mpt) REVERT: X 98 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8332 (pt) REVERT: Z 49 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: Z 85 GLU cc_start: 0.5479 (tt0) cc_final: 0.4945 (tt0) REVERT: c 34 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8184 (mmmt) REVERT: g 27 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8214 (mttm) REVERT: g 106 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7708 (pttt) REVERT: g 113 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8264 (pt0) REVERT: h 13 ASP cc_start: 0.9201 (t0) cc_final: 0.8909 (t0) REVERT: h 16 ARG cc_start: 0.8344 (mtm180) cc_final: 0.8058 (mtm110) REVERT: h 65 GLU cc_start: 0.9101 (tp30) cc_final: 0.8860 (tm-30) REVERT: h 102 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7069 (pt0) REVERT: l 111 ASP cc_start: 0.9269 (OUTLIER) cc_final: 0.8788 (t70) REVERT: l 596 MET cc_start: 0.8591 (mtp) cc_final: 0.8383 (mtp) REVERT: m 77 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: m 139 GLU cc_start: 0.8670 (tt0) cc_final: 0.8372 (tt0) REVERT: o 56 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7058 (ptt-90) REVERT: o 111 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8360 (mtmt) REVERT: p 42 CYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8212 (m) REVERT: r 396 MET cc_start: 0.8609 (mmt) cc_final: 0.7402 (mmt) REVERT: v 53 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8705 (tp) REVERT: v 103 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7977 (tp30) REVERT: w 51 ARG cc_start: 0.8421 (ptp-170) cc_final: 0.8125 (mtm-85) REVERT: w 227 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7734 (mpt) outliers start: 135 outliers final: 69 residues processed: 724 average time/residue: 1.6661 time to fit residues: 1450.8774 Evaluate side-chains 732 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 649 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain e residue 151 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 106 LYS Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 SER Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 288 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 56 ARG Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 244 MET Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 103 GLU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 368 optimal weight: 0.9980 chunk 251 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 329 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 377 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 397 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN d 149 HIS e 148 GLN g 18 ASN h 21 GLN i 49 ASN i 319 HIS l 109 HIS m 86 ASN n 3 ASN r 251 ASN r 304 GLN v 65 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40683 Z= 0.175 Angle : 0.511 8.813 54881 Z= 0.255 Chirality : 0.039 0.215 5931 Planarity : 0.004 0.057 6676 Dihedral : 15.162 166.139 6581 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 2.94 % Allowed : 15.78 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.13), residues: 4666 helix: 2.24 (0.10), residues: 2921 sheet: -0.76 (0.82), residues: 40 loop : -0.68 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.008 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 666 time to evaluate : 4.892 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: S 4 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8549 (mt-10) REVERT: U 62 ASN cc_start: 0.8245 (t0) cc_final: 0.7968 (t160) REVERT: W 98 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7155 (mpt) REVERT: X 98 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8347 (pt) REVERT: Z 49 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: Z 85 GLU cc_start: 0.5502 (tt0) cc_final: 0.4967 (tt0) REVERT: c 34 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8185 (mmmt) REVERT: g 27 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8230 (mttm) REVERT: g 113 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: h 13 ASP cc_start: 0.9161 (t0) cc_final: 0.8868 (t0) REVERT: h 16 ARG cc_start: 0.8351 (mtm180) cc_final: 0.8057 (mtm110) REVERT: h 65 GLU cc_start: 0.9085 (tp30) cc_final: 0.8847 (tm-30) REVERT: h 102 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7063 (pt0) REVERT: i 100 MET cc_start: 0.8750 (mtp) cc_final: 0.8504 (mtp) REVERT: i 263 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.6923 (mttp) REVERT: j 1 MET cc_start: 0.7108 (tpp) cc_final: 0.6833 (tpp) REVERT: l 70 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8950 (m) REVERT: l 111 ASP cc_start: 0.9260 (OUTLIER) cc_final: 0.8772 (t70) REVERT: l 579 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7930 (m-40) REVERT: m 1 MET cc_start: 0.3080 (tpt) cc_final: 0.1973 (ptt) REVERT: m 55 MET cc_start: 0.8868 (tpp) cc_final: 0.8658 (mmp) REVERT: m 77 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: m 81 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: m 139 GLU cc_start: 0.8648 (tt0) cc_final: 0.8387 (tt0) REVERT: o 56 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7037 (ptt-90) REVERT: o 111 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8354 (mtmt) REVERT: p 42 CYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8182 (m) REVERT: r 336 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6651 (mtt180) REVERT: s 70 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8612 (mtm) REVERT: v 53 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8661 (tp) REVERT: v 103 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: w 51 ARG cc_start: 0.8395 (ptp-170) cc_final: 0.8124 (mtm-85) REVERT: w 241 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.6405 (t80) outliers start: 121 outliers final: 59 residues processed: 719 average time/residue: 1.6622 time to fit residues: 1434.4388 Evaluate side-chains 727 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 649 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 128 LEU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 579 ASN Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 56 ARG Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 158 LEU Chi-restraints excluded: chain r residue 244 MET Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 336 ARG Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 70 MET Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 103 GLU Chi-restraints excluded: chain w residue 41 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 148 optimal weight: 0.2980 chunk 398 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 443 optimal weight: 7.9990 chunk 367 optimal weight: 0.0980 chunk 205 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 ASN b 13 GLN g 18 ASN h 21 GLN i 319 HIS l 109 HIS m 86 ASN n 3 ASN r 304 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 40683 Z= 0.152 Angle : 0.500 10.324 54881 Z= 0.249 Chirality : 0.039 0.222 5931 Planarity : 0.004 0.054 6676 Dihedral : 14.353 155.106 6577 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 3.06 % Allowed : 16.02 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.13), residues: 4666 helix: 2.31 (0.10), residues: 2925 sheet: -0.76 (0.83), residues: 40 loop : -0.65 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.007 0.001 HIS r 30 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.014 0.000 ARG w 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 681 time to evaluate : 4.414 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 62 ASN cc_start: 0.8255 (t0) cc_final: 0.7942 (t160) REVERT: W 98 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7184 (mpt) REVERT: Z 85 GLU cc_start: 0.5582 (tt0) cc_final: 0.4964 (tt0) REVERT: c 34 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8044 (mmmt) REVERT: e 146 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8226 (mttp) REVERT: f 73 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8662 (m110) REVERT: g 27 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8253 (mttm) REVERT: g 113 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: h 13 ASP cc_start: 0.9039 (t0) cc_final: 0.8785 (t0) REVERT: h 16 ARG cc_start: 0.8345 (mtm180) cc_final: 0.8047 (mtm110) REVERT: h 65 GLU cc_start: 0.9076 (tp30) cc_final: 0.8842 (tm-30) REVERT: h 102 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7034 (pt0) REVERT: i 263 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.6896 (mttp) REVERT: i 271 THR cc_start: 0.8742 (m) cc_final: 0.8518 (p) REVERT: j 1 MET cc_start: 0.7055 (tpp) cc_final: 0.6778 (tpp) REVERT: l 111 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8748 (t70) REVERT: l 579 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: m 1 MET cc_start: 0.3071 (OUTLIER) cc_final: 0.2041 (ptt) REVERT: m 77 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: m 81 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: o 111 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8396 (mtmt) REVERT: p 42 CYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8210 (m) REVERT: r 336 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.6586 (mtt180) REVERT: s 70 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8579 (mtm) REVERT: v 53 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8535 (tp) REVERT: v 103 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: w 72 ARG cc_start: 0.7790 (ttp-110) cc_final: 0.7277 (ttp80) REVERT: w 223 ASN cc_start: 0.8386 (t0) cc_final: 0.8182 (t0) REVERT: w 241 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.6258 (t80) outliers start: 126 outliers final: 49 residues processed: 738 average time/residue: 1.6267 time to fit residues: 1451.5596 Evaluate side-chains 727 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 661 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 249 SER Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 579 ASN Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 244 MET Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 336 ARG Chi-restraints excluded: chain r residue 454 ILE Chi-restraints excluded: chain s residue 70 MET Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 103 GLU Chi-restraints excluded: chain w residue 41 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 427 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 252 optimal weight: 6.9990 chunk 323 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 373 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 441 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 36 GLN U 11 ASN a 189 ASN b 13 GLN e 148 GLN g 18 ASN h 21 GLN l 109 HIS l 135 ASN l 199 GLN n 3 ASN r 304 GLN v 65 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40683 Z= 0.287 Angle : 0.572 9.438 54881 Z= 0.286 Chirality : 0.042 0.224 5931 Planarity : 0.004 0.060 6676 Dihedral : 14.253 157.242 6572 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.14 % Favored : 95.80 % Rotamer: Outliers : 2.86 % Allowed : 16.63 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.13), residues: 4666 helix: 2.11 (0.10), residues: 2928 sheet: -0.64 (0.84), residues: 40 loop : -0.69 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.007 0.001 HIS v 61 PHE 0.033 0.002 PHE i 292 TYR 0.027 0.001 TYR l 587 ARG 0.007 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 667 time to evaluate : 4.518 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 15 LYS cc_start: 0.8606 (mtmt) cc_final: 0.7923 (mmtp) REVERT: U 62 ASN cc_start: 0.8268 (t0) cc_final: 0.7959 (t160) REVERT: W 98 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7185 (mpt) REVERT: Z 30 GLU cc_start: 0.8440 (tt0) cc_final: 0.7779 (mt-10) REVERT: Z 42 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7786 (ptm160) REVERT: Z 85 GLU cc_start: 0.5731 (tt0) cc_final: 0.5196 (tt0) REVERT: c 34 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8224 (mmmt) REVERT: c 43 LYS cc_start: 0.8350 (mttm) cc_final: 0.8090 (mmtm) REVERT: h 16 ARG cc_start: 0.8361 (mtm180) cc_final: 0.8085 (mtm180) REVERT: h 65 GLU cc_start: 0.9103 (tp30) cc_final: 0.8865 (tm-30) REVERT: h 102 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7054 (pt0) REVERT: i 100 MET cc_start: 0.8712 (mtp) cc_final: 0.8477 (mtt) REVERT: j 1 MET cc_start: 0.7107 (tpp) cc_final: 0.6811 (tpp) REVERT: j 90 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8838 (mmp) REVERT: l 108 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8956 (mmm) REVERT: l 111 ASP cc_start: 0.9278 (OUTLIER) cc_final: 0.8781 (t70) REVERT: m 1 MET cc_start: 0.2868 (tpt) cc_final: 0.2018 (ptt) REVERT: m 77 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: m 81 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: o 111 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8367 (mtmt) REVERT: p 42 CYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8226 (m) REVERT: r 396 MET cc_start: 0.8721 (mmt) cc_final: 0.7278 (mmt) REVERT: s 62 ARG cc_start: 0.8132 (ptt90) cc_final: 0.7640 (ptm160) REVERT: s 70 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8594 (mtm) REVERT: u 157 ASP cc_start: 0.8620 (p0) cc_final: 0.8132 (m-30) REVERT: v 52 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7862 (mtt) REVERT: w 223 ASN cc_start: 0.8273 (t0) cc_final: 0.7224 (t0) REVERT: w 227 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7629 (mpp) outliers start: 118 outliers final: 61 residues processed: 728 average time/residue: 1.6452 time to fit residues: 1435.5737 Evaluate side-chains 720 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 648 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 108 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain m residue 170 GLU Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain s residue 70 MET Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 52 MET Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 145 ASP Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 285 ASP Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 273 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 85 optimal weight: 0.0770 chunk 280 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 346 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 36 GLN U 11 ASN a 189 ASN b 13 GLN g 18 ASN h 21 GLN i 319 HIS l 109 HIS l 135 ASN l 199 GLN m 86 ASN n 3 ASN r 304 GLN v 65 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 40683 Z= 0.157 Angle : 0.516 10.968 54881 Z= 0.258 Chirality : 0.039 0.204 5931 Planarity : 0.004 0.058 6676 Dihedral : 13.749 155.631 6572 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.28 % Allowed : 17.65 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.13), residues: 4666 helix: 2.24 (0.10), residues: 2929 sheet: -0.62 (0.83), residues: 40 loop : -0.62 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 PHE 0.027 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.014 0.000 ARG w 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 673 time to evaluate : 4.283 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 62 ASN cc_start: 0.8285 (t0) cc_final: 0.7982 (t160) REVERT: W 98 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7211 (mpt) REVERT: Z 30 GLU cc_start: 0.8431 (tt0) cc_final: 0.7757 (mt-10) REVERT: Z 42 ARG cc_start: 0.7922 (ptm160) cc_final: 0.7700 (ptm160) REVERT: Z 85 GLU cc_start: 0.5860 (tt0) cc_final: 0.5183 (tt0) REVERT: c 34 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8050 (mmmt) REVERT: c 43 LYS cc_start: 0.8359 (mttm) cc_final: 0.8095 (mmtm) REVERT: g 27 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8194 (mttm) REVERT: g 113 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: h 16 ARG cc_start: 0.8356 (mtm180) cc_final: 0.8076 (mtm110) REVERT: h 65 GLU cc_start: 0.9077 (tp30) cc_final: 0.8756 (tm-30) REVERT: i 263 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.6931 (mttm) REVERT: i 271 THR cc_start: 0.8829 (m) cc_final: 0.8617 (p) REVERT: j 1 MET cc_start: 0.7078 (tpp) cc_final: 0.6774 (tpp) REVERT: l 111 ASP cc_start: 0.9268 (OUTLIER) cc_final: 0.9051 (t0) REVERT: l 475 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7323 (mpt) REVERT: m 1 MET cc_start: 0.2892 (tpt) cc_final: 0.1977 (ptt) REVERT: m 77 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: m 81 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: m 128 TYR cc_start: 0.8049 (m-80) cc_final: 0.6799 (m-80) REVERT: n 30 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7355 (mtt-85) REVERT: o 111 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8354 (mtmt) REVERT: p 42 CYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8189 (m) REVERT: r 336 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6675 (mtt180) REVERT: u 157 ASP cc_start: 0.8618 (p0) cc_final: 0.8179 (m-30) REVERT: w 72 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7344 (ttp80) REVERT: w 120 ASP cc_start: 0.8350 (t70) cc_final: 0.8103 (t70) REVERT: w 223 ASN cc_start: 0.8263 (t0) cc_final: 0.8043 (t0) REVERT: w 241 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.6414 (t80) REVERT: w 264 GLU cc_start: 0.7972 (mp0) cc_final: 0.7678 (mp0) REVERT: w 287 ASP cc_start: 0.7127 (t0) cc_final: 0.6867 (t0) outliers start: 94 outliers final: 46 residues processed: 719 average time/residue: 1.6469 time to fit residues: 1423.4216 Evaluate side-chains 721 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 665 time to evaluate : 4.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain d residue 99 ASP Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 109 LYS Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 117 ASP Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 336 ARG Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 401 optimal weight: 0.9980 chunk 422 optimal weight: 1.9990 chunk 385 optimal weight: 0.7980 chunk 411 optimal weight: 0.4980 chunk 247 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 126 optimal weight: 0.0070 chunk 371 optimal weight: 0.8980 chunk 389 optimal weight: 0.7980 chunk 409 optimal weight: 6.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 36 GLN a 189 ASN b 13 GLN e 148 GLN g 18 ASN h 21 GLN k 57 ASN l 109 HIS l 135 ASN l 199 GLN n 3 ASN r 139 GLN r 304 GLN s 235 ASN v 65 GLN ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 40683 Z= 0.153 Angle : 0.518 12.519 54881 Z= 0.257 Chirality : 0.039 0.201 5931 Planarity : 0.004 0.055 6676 Dihedral : 13.210 155.019 6572 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 1.97 % Allowed : 18.11 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.13), residues: 4666 helix: 2.31 (0.10), residues: 2935 sheet: -0.56 (0.83), residues: 40 loop : -0.59 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.005 0.001 HIS r 30 PHE 0.030 0.001 PHE i 292 TYR 0.020 0.001 TYR r 406 ARG 0.010 0.000 ARG S 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 685 time to evaluate : 4.918 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 62 ASN cc_start: 0.8305 (t0) cc_final: 0.7994 (t160) REVERT: W 98 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7149 (mpt) REVERT: X 129 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: Z 30 GLU cc_start: 0.8412 (tt0) cc_final: 0.7765 (mt-10) REVERT: Z 42 ARG cc_start: 0.7923 (ptm160) cc_final: 0.7705 (ptm160) REVERT: Z 85 GLU cc_start: 0.5835 (tt0) cc_final: 0.5158 (tt0) REVERT: b 99 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: c 34 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8075 (mmmt) REVERT: c 43 LYS cc_start: 0.8365 (mttm) cc_final: 0.8088 (mmtm) REVERT: g 19 GLU cc_start: 0.8324 (pt0) cc_final: 0.8118 (pt0) REVERT: g 113 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: h 13 ASP cc_start: 0.9014 (t0) cc_final: 0.8780 (t0) REVERT: h 16 ARG cc_start: 0.8370 (mtm180) cc_final: 0.8125 (mtm110) REVERT: h 65 GLU cc_start: 0.9076 (tp30) cc_final: 0.8844 (tm-30) REVERT: i 263 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.6934 (mttp) REVERT: i 271 THR cc_start: 0.8918 (m) cc_final: 0.8708 (p) REVERT: j 1 MET cc_start: 0.7046 (tpp) cc_final: 0.6740 (tpp) REVERT: l 383 MET cc_start: 0.8895 (tpt) cc_final: 0.8464 (tpt) REVERT: l 475 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7176 (mpt) REVERT: m 1 MET cc_start: 0.2886 (OUTLIER) cc_final: 0.2027 (ptt) REVERT: m 46 ASN cc_start: 0.8821 (m-40) cc_final: 0.8544 (m-40) REVERT: m 77 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: m 81 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: m 128 TYR cc_start: 0.8061 (m-80) cc_final: 0.6836 (m-80) REVERT: n 30 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7352 (mtt-85) REVERT: o 111 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8346 (mtmt) REVERT: p 42 CYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8212 (m) REVERT: r 336 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6617 (mtt180) REVERT: u 157 ASP cc_start: 0.8593 (p0) cc_final: 0.8139 (m-30) REVERT: w 41 LEU cc_start: 0.8828 (tt) cc_final: 0.8558 (tm) REVERT: w 72 ARG cc_start: 0.7790 (ttp-110) cc_final: 0.7327 (ttp80) REVERT: w 223 ASN cc_start: 0.8348 (t0) cc_final: 0.8014 (t0) REVERT: w 241 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.6272 (t80) REVERT: w 264 GLU cc_start: 0.8009 (mp0) cc_final: 0.7709 (mp0) outliers start: 81 outliers final: 38 residues processed: 723 average time/residue: 1.6717 time to fit residues: 1451.6548 Evaluate side-chains 719 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 669 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 146 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain r residue 336 ARG Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 274 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 270 optimal weight: 5.9990 chunk 434 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 456 optimal weight: 0.4980 chunk 419 optimal weight: 6.9990 chunk 363 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN a 189 ASN b 13 GLN g 18 ASN h 21 GLN l 59 GLN l 109 HIS l 170 GLN ** l 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 ASN r 139 GLN r 304 GLN v 47 ASN v 65 GLN ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 40683 Z= 0.317 Angle : 0.599 9.051 54881 Z= 0.298 Chirality : 0.043 0.232 5931 Planarity : 0.005 0.059 6676 Dihedral : 13.545 157.603 6572 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 1.63 % Allowed : 18.52 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.13), residues: 4666 helix: 2.04 (0.10), residues: 2945 sheet: -0.60 (0.84), residues: 40 loop : -0.67 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP u 86 HIS 0.007 0.001 HIS v 61 PHE 0.033 0.002 PHE i 292 TYR 0.028 0.002 TYR l 587 ARG 0.010 0.000 ARG w 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 659 time to evaluate : 4.593 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 62 ASN cc_start: 0.8253 (t0) cc_final: 0.7893 (t160) REVERT: W 98 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7200 (mpt) REVERT: Z 30 GLU cc_start: 0.8427 (tt0) cc_final: 0.7793 (mt-10) REVERT: Z 85 GLU cc_start: 0.6018 (tt0) cc_final: 0.5320 (tt0) REVERT: c 34 LYS cc_start: 0.8415 (mmmt) cc_final: 0.8085 (mmmt) REVERT: c 43 LYS cc_start: 0.8362 (mttm) cc_final: 0.8094 (mmtm) REVERT: h 16 ARG cc_start: 0.8370 (mtm180) cc_final: 0.8089 (mtm110) REVERT: h 102 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: i 263 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7007 (mttm) REVERT: l 475 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7163 (mpt) REVERT: m 1 MET cc_start: 0.2944 (tpt) cc_final: 0.2070 (ptt) REVERT: m 77 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: m 81 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: n 30 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7431 (mtt-85) REVERT: o 111 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8367 (mtmt) REVERT: p 42 CYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8209 (m) REVERT: u 157 ASP cc_start: 0.8643 (p0) cc_final: 0.8170 (m-30) REVERT: w 72 ARG cc_start: 0.7869 (ttp-110) cc_final: 0.7389 (ttp80) REVERT: w 264 GLU cc_start: 0.8043 (mp0) cc_final: 0.7726 (mp0) REVERT: w 287 ASP cc_start: 0.7138 (t0) cc_final: 0.6888 (t0) REVERT: w 351 TRP cc_start: 0.8322 (m100) cc_final: 0.8009 (m-90) outliers start: 67 outliers final: 46 residues processed: 696 average time/residue: 1.7266 time to fit residues: 1442.3757 Evaluate side-chains 703 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 650 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 11 ASN Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 16 THR Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ASP Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain Z residue 18 ASP Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 96 VAL Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 191 THR Chi-restraints excluded: chain i residue 223 SER Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 273 ASN Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain l residue 8 THR Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain m residue 77 GLU Chi-restraints excluded: chain m residue 81 GLU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 108 LEU Chi-restraints excluded: chain m residue 126 VAL Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 250 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 81 LEU Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 VAL Chi-restraints excluded: chain u residue 74 ILE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain w residue 56 THR Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 297 LEU Chi-restraints excluded: chain w residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 288 optimal weight: 0.7980 chunk 387 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 335 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 chunk 363 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 373 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 33 GLN a 189 ASN b 13 GLN e 148 GLN g 18 ASN h 21 GLN l 109 HIS ** l 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 86 ASN n 3 ASN r 304 GLN v 47 ASN ** w 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.076919 restraints weight = 57831.043| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.79 r_work: 0.2722 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 40683 Z= 0.256 Angle : 0.673 59.198 54881 Z= 0.356 Chirality : 0.041 0.400 5931 Planarity : 0.004 0.059 6676 Dihedral : 13.541 157.550 6572 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 1.65 % Allowed : 18.45 % Favored : 79.90 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.13), residues: 4666 helix: 2.04 (0.10), residues: 2944 sheet: -0.61 (0.84), residues: 40 loop : -0.67 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP u 86 HIS 0.006 0.001 HIS r 30 PHE 0.032 0.001 PHE i 292 TYR 0.028 0.001 TYR l 587 ARG 0.008 0.000 ARG S 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18781.38 seconds wall clock time: 333 minutes 58.36 seconds (20038.36 seconds total)