Starting phenix.real_space_refine on Tue Apr 16 14:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyg_32204/04_2024/7vyg_32204_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyg_32204/04_2024/7vyg_32204.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyg_32204/04_2024/7vyg_32204_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/7vyg_32204/04_2024/7vyg_32204_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyg_32204/04_2024/7vyg_32204_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyg_32204/04_2024/7vyg_32204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyg_32204/04_2024/7vyg_32204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyg_32204/04_2024/7vyg_32204_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyg_32204/04_2024/7vyg_32204_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= 0.006 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 35 5.49 5 S 293 5.16 5 C 26059 2.51 5 N 6282 2.21 5 O 6970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S GLU 4": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "a GLU 103": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 185": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 274": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j GLU 32": "OE1" <-> "OE2" Residue "j GLU 38": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "r GLU 141": "OE1" <-> "OE2" Residue "r GLU 222": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 204": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "v GLU 45": "OE1" <-> "OE2" Residue "w PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 251": "OE1" <-> "OE2" Residue "w GLU 274": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39639 Number of models: 1 Model: "" Number of chains: 46 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: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 699 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 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: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 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: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1292 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 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: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1530 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2502 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "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: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2583 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 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: "j" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 156 Unusual residues: {'PEE': 2, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "l" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 335 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "m" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 95 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "n" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 202 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {' UQ': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 20.79, per 1000 atoms: 0.52 Number of scatterers: 39639 At special positions: 0 Unit cell: (180.466, 195.504, 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 35 15.00 O 6970 8.00 N 6282 7.00 C 26059 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=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.21 Conformation dependent library (CDL) restraints added in 7.2 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: 204 helices and 4 sheets defined 62.1% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.17 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.963A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 60 No H-bonds generated for 'chain 'Q' and resid 58 through 60' Processing helix chain 'S' and resid 2 through 30 removed outlier: 3.636A 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 removed outlier: 3.685A pdb=" N THR S 30 " --> pdb=" O HIS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 54 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 5 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 48 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 97 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 130 through 138 Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.875A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' 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: 3.969A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 53 removed outlier: 4.372A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'a' and resid 62 through 92 removed outlier: 4.253A pdb=" N THR a 78 " --> pdb=" O TYR a 74 " (cutoff:3.500A) Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.732A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 26 Processing helix chain 'b' and resid 70 through 73 No H-bonds generated for 'chain 'b' and resid 70 through 73' Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 59 through 61 No H-bonds generated for 'chain 'c' and resid 59 through 61' Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 129 through 149 Processing helix chain 'd' and resid 29 through 40 Processing helix chain 'd' and resid 42 through 58 removed outlier: 3.611A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.841A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'e' and resid 100 through 107 Processing helix chain 'e' and resid 115 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 19 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.824A 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 43 Processing helix chain 'h' and resid 49 through 55 removed outlier: 3.939A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 88 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.784A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.321A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.789A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix removed outlier: 3.607A pdb=" N GLN i 144 " --> pdb=" O SER i 140 " (cutoff:3.500A) Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.856A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 194 removed outlier: 3.949A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU i 194 " --> pdb=" O MET i 190 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.658A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 270 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.006A pdb=" N LEU i 287 " --> pdb=" O ALA i 283 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU i 296 " --> pdb=" O PHE i 292 " (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 345 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.916A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.492A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 55 through 85 removed outlier: 3.992A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix removed outlier: 4.346A pdb=" N CYS k 69 " --> pdb=" O PHE k 66 " (cutoff:3.500A) 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 15 removed outlier: 3.872A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 17 through 23 removed outlier: 4.876A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.268A 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: 3.846A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.821A pdb=" N GLY l 178 " --> pdb=" O TYR l 174 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.106A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 250 removed outlier: 3.764A pdb=" N HIS l 248 " --> pdb=" O SER l 244 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER l 249 " --> pdb=" O ALA l 245 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER l 250 " --> pdb=" O LEU l 246 " (cutoff:3.500A) Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 267 No H-bonds generated for 'chain 'l' and resid 264 through 267' Processing helix chain 'l' and resid 272 through 294 removed outlier: 3.591A pdb=" N ALA l 289 " --> pdb=" O THR l 285 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) removed outlier: 4.721A 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: 4.116A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 392 through 400 Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.690A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 3.702A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.466A 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: 3.955A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.404A 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: 4.308A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 removed outlier: 3.610A pdb=" N GLN l 546 " --> pdb=" O LEU l 542 " (cutoff:3.500A) Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 602 removed outlier: 3.930A pdb=" N LEU l 589 " --> pdb=" O LYS l 585 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 removed outlier: 3.513A pdb=" N PHE m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 74 removed outlier: 4.562A pdb=" N GLY m 62 " --> pdb=" O LEU m 58 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA m 73 " --> pdb=" O GLY m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 109 Processing helix chain 'm' and resid 138 through 149 removed outlier: 4.149A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER m 148 " --> pdb=" O ALA m 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 removed outlier: 3.523A pdb=" N ARG m 173 " --> pdb=" O MET m 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 11 removed outlier: 4.779A pdb=" N ASP n 10 " --> pdb=" O GLN n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 34 removed outlier: 3.642A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.715A 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 117 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: 4.563A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 142 removed outlier: 3.625A pdb=" N SER p 132 " --> pdb=" O LEU p 128 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP p 133 " --> pdb=" O ARG p 129 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.605A 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 removed outlier: 4.252A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.168A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.671A 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 removed outlier: 3.806A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 110 Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.848A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 142 through 171 removed outlier: 3.811A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.554A 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 204 removed outlier: 4.127A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.098A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL r 221 " --> pdb=" O PRO r 217 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 250 removed outlier: 4.944A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.838A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 4.225A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 4.134A pdb=" N LEU r 296 " --> pdb=" O SER r 292 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL r 297 " --> pdb=" O HIS r 293 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.506A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 4.407A pdb=" N THR r 403 " --> pdb=" O MET r 400 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR r 413 " --> pdb=" O MET r 410 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 448 Proline residue: r 443 - end of helix removed outlier: 3.770A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (cutoff:3.500A) 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: 3.699A 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: 4.471A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 3.870A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.002A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 162 through 168 removed outlier: 3.661A pdb=" N ILE s 166 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 removed outlier: 3.696A pdb=" N MET s 184 " --> pdb=" O PRO s 180 " (cutoff:3.500A) 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 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 274 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.698A 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 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 57 through 77 Processing helix chain 'u' and resid 80 through 91 removed outlier: 3.713A pdb=" N CYS u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 115 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 81 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 97 Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 167 through 175 Processing helix chain 'w' and resid 181 through 192 Processing helix chain 'w' and resid 195 through 197 No H-bonds generated for 'chain 'w' and resid 195 through 197' Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 250 Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 304 No H-bonds generated for 'chain 'w' and resid 301 through 304' Processing helix chain 'w' and resid 306 through 309 removed outlier: 3.875A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 309' Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 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: 6.621A 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: 6.429A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'w' and resid 84 through 86 1968 hydrogen bonds defined for protein. 5643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.86 Time building geometry restraints manager: 16.88 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: 5978 1.31 - 1.44: 10999 1.44 - 1.58: 23022 1.58 - 1.71: 120 1.71 - 1.84: 529 Bond restraints: 40648 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C18 UQ s 402 " pdb=" C19 UQ s 402 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CA7 CDL m 201 " pdb=" OA8 CDL m 201 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CB7 CDL m 201 " pdb=" OB8 CDL m 201 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.13e+02 bond pdb=" C13 UQ s 402 " pdb=" C14 UQ s 402 " ideal model delta sigma weight residual 1.335 1.547 -0.212 2.00e-02 2.50e+03 1.13e+02 ... (remaining 40643 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.08: 1044 105.08 - 112.45: 21023 112.45 - 119.81: 14282 119.81 - 127.18: 17912 127.18 - 134.55: 588 Bond angle restraints: 54849 Sorted by residual: angle pdb=" C51 CDL m 201 " pdb=" CB5 CDL m 201 " pdb=" OB6 CDL m 201 " ideal model delta sigma weight residual 111.33 120.27 -8.94 1.32e+00 5.72e-01 4.58e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.25 -8.92 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C51 CDL s 401 " pdb=" CB5 CDL s 401 " pdb=" OB6 CDL s 401 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL V 202 " pdb=" CA5 CDL V 202 " pdb=" OA6 CDL V 202 " ideal model delta sigma weight residual 111.33 120.18 -8.85 1.32e+00 5.72e-01 4.48e+01 angle pdb=" C11 CDL V 201 " pdb=" CA5 CDL V 201 " pdb=" OA6 CDL V 201 " ideal model delta sigma weight residual 111.33 120.16 -8.83 1.32e+00 5.72e-01 4.47e+01 ... (remaining 54844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 23766 34.74 - 69.47: 866 69.47 - 104.21: 75 104.21 - 138.95: 10 138.95 - 173.68: 13 Dihedral angle restraints: 24730 sinusoidal: 10869 harmonic: 13861 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual 300.00 126.32 173.68 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CB CYS u 78 " pdb=" SG CYS u 78 " pdb=" SG CYS u 110 " pdb=" CB CYS u 110 " ideal model delta sinusoidal sigma weight residual -86.00 -143.81 57.81 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CB CYS d 113 " pdb=" SG CYS d 113 " pdb=" SG CYS d 125 " pdb=" CB CYS d 125 " ideal model delta sinusoidal sigma weight residual -86.00 -132.91 46.91 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 24727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5393 0.072 - 0.145: 504 0.145 - 0.217: 22 0.217 - 0.289: 7 0.289 - 0.361: 4 Chirality restraints: 5930 Sorted by residual: chirality pdb=" CA TYR m 60 " pdb=" N TYR m 60 " pdb=" C TYR m 60 " pdb=" CB TYR m 60 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA LYS m 23 " pdb=" N LYS m 23 " pdb=" C LYS m 23 " pdb=" CB LYS m 23 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CG LEU g 16 " pdb=" CB LEU g 16 " pdb=" CD1 LEU g 16 " pdb=" CD2 LEU g 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 5927 not shown) Planarity restraints: 6675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.075 2.00e-02 2.50e+03 2.66e-01 8.86e+02 pdb=" C11 UQ s 402 " 0.098 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.253 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.468 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " -0.237 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.176 2.00e-02 2.50e+03 2.12e-01 5.64e+02 pdb=" C18 UQ s 402 " -0.114 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.347 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.042 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " -0.105 2.00e-02 2.50e+03 1.63e-01 3.34e+02 pdb=" C13 UQ s 402 " 0.037 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " 0.297 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " -0.055 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " -0.174 2.00e-02 2.50e+03 ... (remaining 6672 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2947 2.74 - 3.28: 39272 3.28 - 3.82: 67463 3.82 - 4.36: 83079 4.36 - 4.90: 141025 Nonbonded interactions: 333786 Sorted by model distance: nonbonded pdb=" OH TYR n 26 " pdb=" NH2 ARG n 30 " model vdw 2.197 2.520 nonbonded pdb=" OG1 THR r 357 " pdb=" O1 CDL l 702 " model vdw 2.199 2.440 nonbonded pdb=" O ASP Y 76 " pdb=" OH TYR l 385 " model vdw 2.209 2.440 nonbonded pdb=" OH TYR l 515 " pdb=" OE2 GLU p 70 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.218 2.440 ... (remaining 333781 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.550 Check model and map are aligned: 0.580 Set scattering table: 0.380 Process input model: 102.530 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.008 0.226 40648 Z= 0.497 Angle : 0.849 16.983 54849 Z= 0.424 Chirality : 0.044 0.361 5930 Planarity : 0.007 0.266 6675 Dihedral : 17.432 173.684 15752 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 0.17 % Allowed : 0.39 % Favored : 99.44 % 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: 1.36 (0.12), residues: 4666 helix: 1.78 (0.10), residues: 2933 sheet: -1.01 (0.99), residues: 23 loop : -0.60 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.008 0.001 HIS S 27 PHE 0.029 0.002 PHE s 270 TYR 0.023 0.001 TYR s 282 ARG 0.003 0.000 ARG W 68 *********************** 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 794 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 787 time to evaluate : 4.582 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: d 73 ASP cc_start: 0.7906 (p0) cc_final: 0.7306 (p0) REVERT: f 53 PHE cc_start: 0.8492 (t80) cc_final: 0.8085 (t80) REVERT: h 18 MET cc_start: 0.8400 (ttt) cc_final: 0.8164 (ttt) REVERT: i 89 MET cc_start: 0.8320 (tpt) cc_final: 0.7587 (tpt) REVERT: k 97 GLN cc_start: 0.8469 (mp10) cc_final: 0.8236 (mp10) REVERT: l 163 ASP cc_start: 0.7798 (m-30) cc_final: 0.7575 (m-30) REVERT: r 401 MET cc_start: 0.8745 (ttp) cc_final: 0.8519 (ttm) REVERT: u 9 THR cc_start: 0.9131 (p) cc_final: 0.8870 (p) outliers start: 7 outliers final: 5 residues processed: 792 average time/residue: 1.7573 time to fit residues: 1659.0634 Evaluate side-chains 660 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 655 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 19 TYR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain l residue 401 MET Chi-restraints excluded: chain m residue 23 LYS Chi-restraints excluded: chain m residue 148 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 386 optimal weight: 9.9990 chunk 347 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 234 optimal weight: 0.1980 chunk 185 optimal weight: 0.9980 chunk 358 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 415 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN b 89 HIS c 160 GLN i 150 ASN j 26 GLN l 351 ASN l 405 ASN m 46 ASN p 62 GLN r 103 GLN r 138 ASN u 64 ASN u 77 HIS v 47 ASN v 76 ASN w 202 HIS w 322 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40648 Z= 0.173 Angle : 0.541 8.973 54849 Z= 0.266 Chirality : 0.040 0.294 5930 Planarity : 0.004 0.044 6675 Dihedral : 16.761 167.558 6530 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 1.72 % Allowed : 8.77 % Favored : 89.50 % 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: 1.62 (0.13), residues: 4666 helix: 1.98 (0.10), residues: 2942 sheet: -0.97 (1.01), residues: 23 loop : -0.50 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.006 0.001 HIS u 77 PHE 0.027 0.001 PHE i 292 TYR 0.027 0.001 TYR l 422 ARG 0.007 0.000 ARG m 173 *********************** 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 761 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 690 time to evaluate : 4.768 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 52 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7897 (mmt) REVERT: U 16 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: V 50 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7224 (tp) REVERT: W 94 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: W 108 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: a 69 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8098 (pttt) REVERT: f 53 PHE cc_start: 0.8503 (t80) cc_final: 0.8096 (t80) REVERT: g 21 ARG cc_start: 0.8448 (mtp180) cc_final: 0.8169 (mtp85) REVERT: h 18 MET cc_start: 0.8372 (ttt) cc_final: 0.8117 (ttt) REVERT: h 55 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: i 245 MET cc_start: 0.8721 (tmm) cc_final: 0.8392 (ttp) REVERT: i 321 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7273 (mmmt) REVERT: k 97 GLN cc_start: 0.8510 (mp10) cc_final: 0.8158 (mp10) REVERT: l 163 ASP cc_start: 0.7777 (m-30) cc_final: 0.7555 (m-30) REVERT: l 383 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8787 (tpt) REVERT: l 598 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8508 (m) REVERT: m 98 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6578 (mmp) REVERT: n 30 ARG cc_start: 0.8199 (mtp180) cc_final: 0.7950 (ttt-90) REVERT: o 19 ASP cc_start: 0.8199 (t0) cc_final: 0.7932 (t0) REVERT: r 378 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: r 401 MET cc_start: 0.8710 (ttp) cc_final: 0.8469 (ttm) REVERT: s 58 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8662 (tttt) REVERT: v 81 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7818 (mmpt) outliers start: 71 outliers final: 27 residues processed: 723 average time/residue: 1.7702 time to fit residues: 1530.9799 Evaluate side-chains 700 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 660 time to evaluate : 4.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 598 SER Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 58 LYS Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain v residue 108 LEU Chi-restraints excluded: chain w residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 231 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 346 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 416 optimal weight: 5.9990 chunk 450 optimal weight: 0.5980 chunk 371 optimal weight: 0.2980 chunk 413 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 334 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 160 GLN i 150 ASN j 26 GLN l 405 ASN r 44 GLN r 103 GLN r 304 GLN s 258 ASN u 77 HIS v 76 ASN v 84 GLN w 202 HIS w 286 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40648 Z= 0.290 Angle : 0.576 8.640 54849 Z= 0.285 Chirality : 0.043 0.281 5930 Planarity : 0.005 0.043 6675 Dihedral : 15.920 156.746 6518 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 2.38 % Allowed : 10.40 % Favored : 87.22 % 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: 1.47 (0.12), residues: 4666 helix: 1.85 (0.10), residues: 2948 sheet: -1.16 (0.97), residues: 23 loop : -0.54 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.009 0.001 HIS u 77 PHE 0.028 0.002 PHE i 292 TYR 0.025 0.002 TYR l 587 ARG 0.008 0.000 ARG b 16 *********************** 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 765 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 667 time to evaluate : 4.529 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 52 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7974 (mmt) REVERT: U 16 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: W 108 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: a 69 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8080 (pttt) REVERT: b 16 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7838 (mtt-85) REVERT: b 93 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7887 (mttp) REVERT: d 42 ASP cc_start: 0.8662 (t0) cc_final: 0.8324 (t0) REVERT: h 55 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: i 89 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7940 (tpt) REVERT: i 245 MET cc_start: 0.8750 (tmm) cc_final: 0.8425 (ttp) REVERT: k 97 GLN cc_start: 0.8565 (mp10) cc_final: 0.8030 (mp10) REVERT: l 59 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7808 (tp40) REVERT: l 163 ASP cc_start: 0.7741 (m-30) cc_final: 0.7506 (m-30) REVERT: l 383 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8820 (tpt) REVERT: n 30 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7851 (ttt-90) REVERT: o 19 ASP cc_start: 0.8321 (t0) cc_final: 0.8087 (t0) REVERT: r 378 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: w 88 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8225 (tt0) outliers start: 98 outliers final: 45 residues processed: 711 average time/residue: 1.7497 time to fit residues: 1486.4828 Evaluate side-chains 707 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 651 time to evaluate : 4.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 60 ARG Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 61 MET Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain v residue 108 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 88 GLU Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 411 optimal weight: 5.9990 chunk 313 optimal weight: 0.2980 chunk 216 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 chunk 198 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 418 optimal weight: 9.9990 chunk 442 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 396 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN i 150 ASN j 26 GLN l 405 ASN r 44 GLN r 103 GLN r 304 GLN v 76 ASN w 202 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40648 Z= 0.174 Angle : 0.519 10.909 54849 Z= 0.257 Chirality : 0.040 0.273 5930 Planarity : 0.004 0.042 6675 Dihedral : 15.022 152.766 6518 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 2.11 % Allowed : 11.88 % Favored : 86.01 % 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: 2.01 (0.10), residues: 2934 sheet: -1.09 (1.00), residues: 23 loop : -0.49 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 86 HIS 0.006 0.001 HIS u 77 PHE 0.027 0.001 PHE i 292 TYR 0.022 0.001 TYR l 422 ARG 0.005 0.000 ARG b 16 *********************** 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 762 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 675 time to evaluate : 5.002 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 16 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8046 (mm-30) REVERT: U 41 TYR cc_start: 0.8551 (m-80) cc_final: 0.8250 (m-10) REVERT: W 108 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: Y 94 ASP cc_start: 0.7914 (m-30) cc_final: 0.7583 (t0) REVERT: a 71 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8709 (ttm) REVERT: b 93 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7873 (mttp) REVERT: c 63 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: d 42 ASP cc_start: 0.8597 (t0) cc_final: 0.8269 (t0) REVERT: d 172 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6548 (mt-10) REVERT: f 53 PHE cc_start: 0.8520 (t80) cc_final: 0.8082 (t80) REVERT: h 55 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: i 89 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7930 (tpt) REVERT: i 245 MET cc_start: 0.8741 (tmm) cc_final: 0.8440 (ttp) REVERT: i 321 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7322 (mmmt) REVERT: k 97 GLN cc_start: 0.8580 (mp10) cc_final: 0.8130 (mp10) REVERT: l 59 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7824 (tp40) REVERT: l 163 ASP cc_start: 0.7776 (m-30) cc_final: 0.7545 (m-30) REVERT: l 383 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8753 (tpt) REVERT: m 98 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6768 (mmp) REVERT: n 30 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7987 (mmt90) REVERT: r 378 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: u 157 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6637 (m-30) outliers start: 87 outliers final: 34 residues processed: 714 average time/residue: 1.7779 time to fit residues: 1515.9874 Evaluate side-chains 704 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 656 time to evaluate : 4.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 13 GLN Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 575 ILE Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 368 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 329 optimal weight: 0.2980 chunk 182 optimal weight: 3.9990 chunk 377 optimal weight: 0.9990 chunk 306 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 226 optimal weight: 2.9990 chunk 397 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 160 GLN i 150 ASN j 26 GLN l 405 ASN l 580 GLN p 62 GLN r 44 GLN r 103 GLN r 304 GLN u 77 HIS v 44 GLN v 76 ASN w 188 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40648 Z= 0.209 Angle : 0.536 8.127 54849 Z= 0.265 Chirality : 0.040 0.270 5930 Planarity : 0.004 0.043 6675 Dihedral : 14.606 150.608 6518 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 2.45 % Allowed : 12.41 % Favored : 85.13 % 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 (0.12), residues: 4666 helix: 1.97 (0.10), residues: 2941 sheet: -1.12 (0.99), residues: 23 loop : -0.50 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.007 0.001 HIS u 77 PHE 0.028 0.001 PHE i 292 TYR 0.023 0.001 TYR l 587 ARG 0.011 0.000 ARG b 16 *********************** 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 766 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 665 time to evaluate : 4.523 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 16 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: U 41 TYR cc_start: 0.8555 (m-80) cc_final: 0.8277 (m-10) REVERT: V 83 LYS cc_start: 0.8073 (mmpt) cc_final: 0.7697 (tptp) REVERT: W 94 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: W 108 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: Y 94 ASP cc_start: 0.7876 (m-30) cc_final: 0.7628 (t0) REVERT: a 71 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8709 (ttm) REVERT: b 93 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7885 (mttp) REVERT: d 172 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6615 (mt-10) REVERT: f 53 PHE cc_start: 0.8531 (t80) cc_final: 0.8086 (t80) REVERT: h 32 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7425 (ttm170) REVERT: h 55 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: i 89 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7966 (tpt) REVERT: i 237 MET cc_start: 0.8644 (mtm) cc_final: 0.8358 (ptp) REVERT: i 245 MET cc_start: 0.8774 (tmm) cc_final: 0.8441 (ttp) REVERT: i 321 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7321 (mmmt) REVERT: k 97 GLN cc_start: 0.8610 (mp10) cc_final: 0.8132 (mp10) REVERT: l 59 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7820 (tp40) REVERT: l 163 ASP cc_start: 0.7801 (m-30) cc_final: 0.7572 (m-30) REVERT: l 207 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5325 (pp20) REVERT: m 98 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6778 (mmp) REVERT: n 30 ARG cc_start: 0.8239 (mtp180) cc_final: 0.8024 (mmt90) REVERT: p 142 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7116 (mt-10) REVERT: r 378 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: s 224 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: u 157 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: v 81 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7854 (mmpt) REVERT: w 88 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8239 (tt0) outliers start: 101 outliers final: 49 residues processed: 710 average time/residue: 1.7852 time to fit residues: 1512.4954 Evaluate side-chains 709 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 643 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 172 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 207 GLU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 575 ILE Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain s residue 231 ILE Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 88 GLU Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 148 optimal weight: 1.9990 chunk 398 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 443 optimal weight: 5.9990 chunk 367 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN i 150 ASN j 26 GLN l 405 ASN r 44 GLN r 103 GLN r 304 GLN u 77 HIS v 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40648 Z= 0.245 Angle : 0.555 8.160 54849 Z= 0.275 Chirality : 0.041 0.271 5930 Planarity : 0.004 0.042 6675 Dihedral : 14.366 150.050 6518 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 2.48 % Allowed : 13.07 % Favored : 84.45 % 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: 1.52 (0.12), residues: 4666 helix: 1.90 (0.10), residues: 2947 sheet: -1.22 (0.97), residues: 23 loop : -0.55 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP u 86 HIS 0.007 0.001 HIS u 77 PHE 0.028 0.002 PHE i 292 TYR 0.024 0.001 TYR l 587 ARG 0.011 0.000 ARG b 16 *********************** 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 766 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 664 time to evaluate : 4.771 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 16 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: U 41 TYR cc_start: 0.8598 (m-80) cc_final: 0.8243 (m-10) REVERT: W 94 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: W 108 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: Y 94 ASP cc_start: 0.7898 (m-30) cc_final: 0.7668 (t0) REVERT: a 69 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8122 (pttt) REVERT: a 71 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8721 (ttm) REVERT: b 93 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7887 (mttp) REVERT: f 53 PHE cc_start: 0.8535 (t80) cc_final: 0.8113 (t80) REVERT: h 32 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7428 (ttm170) REVERT: h 55 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: i 89 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7933 (tpt) REVERT: i 208 TYR cc_start: 0.9099 (t80) cc_final: 0.8866 (t80) REVERT: i 237 MET cc_start: 0.8657 (mtm) cc_final: 0.8378 (ptp) REVERT: i 245 MET cc_start: 0.8772 (tmm) cc_final: 0.8428 (ttp) REVERT: i 321 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7327 (mmmt) REVERT: k 97 GLN cc_start: 0.8601 (mp10) cc_final: 0.8332 (mp10) REVERT: l 59 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7756 (tp40) REVERT: l 163 ASP cc_start: 0.7713 (m-30) cc_final: 0.7489 (m-30) REVERT: l 207 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5402 (pp20) REVERT: l 580 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.6400 (mp-120) REVERT: m 46 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8005 (t0) REVERT: m 98 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6784 (mmp) REVERT: r 304 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: r 378 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: s 202 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: s 224 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: u 157 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6627 (m-30) REVERT: v 81 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7870 (mmpt) REVERT: w 88 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8219 (tt0) outliers start: 102 outliers final: 47 residues processed: 715 average time/residue: 1.8093 time to fit residues: 1558.5924 Evaluate side-chains 714 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 646 time to evaluate : 5.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 51 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 207 GLU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 575 ILE Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain m residue 46 ASN Chi-restraints excluded: chain m residue 98 MET Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 304 GLN Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 224 PHE Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 88 GLU Chi-restraints excluded: chain w residue 287 ASP 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: 1.9990 chunk 252 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 373 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 441 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 11 ASN ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 13 GLN c 160 GLN j 26 GLN l 405 ASN r 44 GLN r 103 GLN r 304 GLN u 77 HIS v 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 40648 Z= 0.367 Angle : 0.627 9.149 54849 Z= 0.311 Chirality : 0.045 0.302 5930 Planarity : 0.005 0.044 6675 Dihedral : 14.609 176.138 6518 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 2.79 % Allowed : 13.34 % Favored : 83.87 % 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: 1.28 (0.12), residues: 4666 helix: 1.70 (0.10), residues: 2953 sheet: -1.41 (0.93), residues: 23 loop : -0.61 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP u 86 HIS 0.009 0.001 HIS u 77 PHE 0.029 0.002 PHE i 292 TYR 0.028 0.002 TYR l 587 ARG 0.010 0.000 ARG b 16 *********************** 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 769 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 654 time to evaluate : 4.945 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 16 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: U 41 TYR cc_start: 0.8671 (m-80) cc_final: 0.8321 (m-10) REVERT: W 94 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: W 96 ILE cc_start: 0.8213 (mm) cc_final: 0.7985 (mt) REVERT: W 108 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: Y 94 ASP cc_start: 0.7930 (m-30) cc_final: 0.7632 (t0) REVERT: a 69 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8137 (pttt) REVERT: a 71 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8731 (ttm) REVERT: b 93 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7928 (mttp) REVERT: h 32 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7671 (ttm170) REVERT: h 42 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: h 55 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: i 89 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8142 (tpt) REVERT: i 208 TYR cc_start: 0.9123 (t80) cc_final: 0.8880 (t80) REVERT: i 237 MET cc_start: 0.8698 (mtm) cc_final: 0.8443 (ptp) REVERT: i 245 MET cc_start: 0.8794 (tmm) cc_final: 0.8451 (ttp) REVERT: k 97 GLN cc_start: 0.8668 (mp10) cc_final: 0.8374 (mp10) REVERT: l 59 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7804 (tp40) REVERT: l 163 ASP cc_start: 0.7710 (m-30) cc_final: 0.7505 (m-30) REVERT: l 207 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5553 (pp20) REVERT: l 580 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.6395 (mp-120) REVERT: m 33 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8657 (tp) REVERT: o 118 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7021 (pt0) REVERT: p 70 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8069 (tp30) REVERT: r 378 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: s 202 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: u 157 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6631 (m-30) REVERT: v 81 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7919 (mmpt) REVERT: w 45 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8052 (pp) REVERT: w 88 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8247 (tt0) outliers start: 115 outliers final: 62 residues processed: 710 average time/residue: 1.7512 time to fit residues: 1482.0884 Evaluate side-chains 723 residues out of total 4156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 640 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain U residue 16 GLU Chi-restraints excluded: chain U residue 22 SER Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 129 THR Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain b residue 93 LYS Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain d residue 41 VAL Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 51 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 16 LEU Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 55 GLU Chi-restraints excluded: chain h residue 85 LYS Chi-restraints excluded: chain i residue 85 THR Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 187 MET Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 159 HIS Chi-restraints excluded: chain l residue 207 GLU Chi-restraints excluded: chain l residue 252 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 477 VAL Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 575 ILE Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain m residue 33 LEU Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain m residue 138 GLU Chi-restraints excluded: chain m residue 148 SER Chi-restraints excluded: chain m residue 163 ILE Chi-restraints excluded: chain n residue 25 CYS Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain o residue 41 SER Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain p residue 70 GLU Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 9 THR Chi-restraints excluded: chain r residue 104 LEU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 310 MET Chi-restraints excluded: chain r residue 355 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 157 ASP Chi-restraints excluded: chain u residue 165 SER Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 53 LEU Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 88 GLU Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 273 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 280 optimal weight: 8.9990 chunk 300 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 346 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: