Starting phenix.real_space_refine on Fri Mar 22 10:45:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/03_2024/6yt9_10914.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/03_2024/6yt9_10914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/03_2024/6yt9_10914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/03_2024/6yt9_10914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/03_2024/6yt9_10914.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt9_10914/03_2024/6yt9_10914.pdb" } resolution = 2.7 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= 0.008 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: 6 Type Number sf(0) Gaussians P 1040 5.49 5 Mg 56 5.21 5 S 28 5.16 5 C 16706 2.51 5 N 6236 2.21 5 O 9213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "e TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 15": "OE1" <-> "OE2" Residue "e ASP 18": "OD1" <-> "OD2" Residue "e TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 90": "OE1" <-> "OE2" Residue "e ASP 101": "OD1" <-> "OD2" Residue "e ARG 123": "NH1" <-> "NH2" Residue "e ARG 131": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "e GLU 174": "OE1" <-> "OE2" Residue "e GLU 181": "OE1" <-> "OE2" Residue "e PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 190": "NH1" <-> "NH2" Residue "e ASP 192": "OD1" <-> "OD2" Residue "e TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 12": "OE1" <-> "OE2" Residue "f PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 49": "NH1" <-> "NH2" Residue "f GLU 54": "OE1" <-> "OE2" Residue "f ASP 74": "OD1" <-> "OD2" Residue "f TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 115": "OE1" <-> "OE2" Residue "f ASP 145": "OD1" <-> "OD2" Residue "f GLU 161": "OE1" <-> "OE2" Residue "f GLU 162": "OE1" <-> "OE2" Residue "g GLU 31": "OE1" <-> "OE2" Residue "g TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 72": "OD1" <-> "OD2" Residue "g ASP 82": "OD1" <-> "OD2" Residue "g GLU 93": "OE1" <-> "OE2" Residue "g GLU 99": "OE1" <-> "OE2" Residue "i GLU 50": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 55": "OE1" <-> "OE2" Residue "i TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 74": "OE1" <-> "OE2" Residue "i ASP 91": "OD1" <-> "OD2" Residue "i ASP 114": "OD1" <-> "OD2" Residue "l GLU 17": "OE1" <-> "OE2" Residue "l TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 82": "OD1" <-> "OD2" Residue "m TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 76": "OE1" <-> "OE2" Residue "p ASP 7": "OD1" <-> "OD2" Residue "p GLU 10": "OE1" <-> "OE2" Residue "p PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 38": "OD1" <-> "OD2" Residue "p GLU 76": "OE1" <-> "OE2" Residue "q TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 28": "NH1" <-> "NH2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "q ASP 55": "OD1" <-> "OD2" Residue "q PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 16": "OD1" <-> "OD2" Residue "r GLU 27": "OE1" <-> "OE2" Residue "r ARG 28": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 40": "NH1" <-> "NH2" Residue "r ARG 41": "NH1" <-> "NH2" Residue "r ASP 58": "OD1" <-> "OD2" Residue "r ARG 66": "NH1" <-> "NH2" Residue "s TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 27": "OD1" <-> "OD2" Residue "s GLU 35": "OE1" <-> "OE2" Residue "s TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 12": "NH1" <-> "NH2" Residue "u TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 34": "NH1" <-> "NH2" Residue "u ASP 43": "OD1" <-> "OD2" Residue "u ASP 63": "OD1" <-> "OD2" Residue "v TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33279 Number of models: 1 Model: "" Number of chains: 17 Chain: "2" Number of atoms: 19228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 19228 Classifications: {'RNA': 894} Modifications used: {'rna2p_pur': 73, 'rna2p_pyr': 39, 'rna3p_pur': 456, 'rna3p_pyr': 326} Link IDs: {'rna2p': 112, 'rna3p': 781} Chain breaks: 3 Chain: "4" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3129 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 73, 'rna3p_pyr': 59} Link IDs: {'rna2p': 14, 'rna3p': 131} Chain: "c" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1079 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 7, 'TRANS': 211} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 669 Unresolved non-hydrogen angles: 854 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 372 Chain: "e" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1592 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 200} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "f" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "g" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 858 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "i" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "l" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 836 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "p" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "q" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "r" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "s" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 434 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "u" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "v" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 389 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "2" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "4" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 16.73, per 1000 atoms: 0.50 Number of scatterers: 33279 At special positions: 0 Unit cell: (167.205, 188.505, 174.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 1040 15.00 Mg 56 11.99 O 9213 8.00 N 6236 7.00 C 16706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 16.69 Conformation dependent library (CDL) restraints added in 2.4 seconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 41.3% alpha, 19.1% beta 368 base pairs and 597 stacking pairs defined. Time for finding SS restraints: 16.95 Creating SS restraints... Processing helix chain 'c' and resid 11 through 15 removed outlier: 3.823A pdb=" N GLY c 15 " --> pdb=" O LEU c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 30 removed outlier: 3.644A pdb=" N ARG c 30 " --> pdb=" O PRO c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 65 removed outlier: 3.981A pdb=" N ASP c 54 " --> pdb=" O PRO c 50 " (cutoff:3.500A) Processing helix chain 'c' and resid 78 through 88 removed outlier: 3.894A pdb=" N ARG c 83 " --> pdb=" O SER c 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 105 through 120 removed outlier: 3.699A pdb=" N GLN c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER c 112 " --> pdb=" O THR c 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG c 115 " --> pdb=" O GLN c 111 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 removed outlier: 3.710A pdb=" N GLN c 124 " --> pdb=" O GLN c 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP c 125 " --> pdb=" O THR c 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 120 through 125' Processing helix chain 'c' and resid 135 through 151 removed outlier: 4.303A pdb=" N ARG c 139 " --> pdb=" O GLU c 135 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER c 149 " --> pdb=" O LYS c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 171 through 181 Processing helix chain 'c' and resid 208 through 224 Processing helix chain 'e' and resid 8 through 16 removed outlier: 3.532A pdb=" N SER e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 53 through 66 Processing helix chain 'e' and resid 70 through 82 Processing helix chain 'e' and resid 87 through 98 Processing helix chain 'e' and resid 99 through 108 Processing helix chain 'e' and resid 114 through 122 removed outlier: 3.576A pdb=" N VAL e 120 " --> pdb=" O ALA e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 152 removed outlier: 3.774A pdb=" N LYS e 152 " --> pdb=" O GLU e 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 149 through 152' Processing helix chain 'e' and resid 154 through 165 removed outlier: 3.801A pdb=" N LYS e 158 " --> pdb=" O GLN e 154 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU e 162 " --> pdb=" O LYS e 158 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU e 163 " --> pdb=" O ASN e 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA e 165 " --> pdb=" O ILE e 161 " (cutoff:3.500A) Processing helix chain 'e' and resid 198 through 206 removed outlier: 4.064A pdb=" N ILE e 202 " --> pdb=" O ASN e 198 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 67 Processing helix chain 'f' and resid 108 through 117 removed outlier: 3.545A pdb=" N ALA f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL f 113 " --> pdb=" O ALA f 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 131 through 146 Processing helix chain 'f' and resid 148 through 157 Processing helix chain 'g' and resid 13 through 17 removed outlier: 4.080A pdb=" N ASP g 16 " --> pdb=" O ASP g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 31 removed outlier: 3.563A pdb=" N GLU g 23 " --> pdb=" O VAL g 19 " (cutoff:3.500A) Processing helix chain 'g' and resid 67 through 80 Processing helix chain 'i' and resid 6 through 20 Processing helix chain 'i' and resid 30 through 43 removed outlier: 3.617A pdb=" N VAL i 39 " --> pdb=" O ALA i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 120 Processing helix chain 'l' and resid 58 through 74 Processing helix chain 'l' and resid 75 through 77 No H-bonds generated for 'chain 'l' and resid 75 through 77' Processing helix chain 'l' and resid 92 through 100 removed outlier: 4.122A pdb=" N VAL l 96 " --> pdb=" O ARG l 92 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 10 Processing helix chain 'm' and resid 21 through 25 removed outlier: 3.543A pdb=" N LYS m 25 " --> pdb=" O PRO m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 118 removed outlier: 3.640A pdb=" N GLY m 118 " --> pdb=" O SER m 115 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 39 Processing helix chain 'p' and resid 39 through 46 removed outlier: 3.681A pdb=" N ALA p 45 " --> pdb=" O GLY p 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 74 removed outlier: 3.553A pdb=" N ARG p 54 " --> pdb=" O HIS p 50 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY p 55 " --> pdb=" O HIS p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 74 through 86 removed outlier: 3.590A pdb=" N TYR p 78 " --> pdb=" O ASP p 74 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 63 Processing helix chain 'q' and resid 68 through 78 Processing helix chain 's' and resid 25 through 30 Processing helix chain 's' and resid 31 through 33 No H-bonds generated for 'chain 's' and resid 31 through 33' Processing helix chain 's' and resid 41 through 46 Processing helix chain 's' and resid 48 through 65 Processing helix chain 'u' and resid 4 through 42 Processing helix chain 'u' and resid 43 through 64 Proline residue: u 56 - end of helix Processing helix chain 'u' and resid 68 through 85 removed outlier: 3.541A pdb=" N ALA u 85 " --> pdb=" O ALA u 81 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 26 removed outlier: 3.527A pdb=" N ARG v 17 " --> pdb=" O ASP v 13 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU v 24 " --> pdb=" O LYS v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 34 Processing helix chain 'v' and resid 40 through 60 Processing sheet with id=AA1, first strand: chain 'c' and resid 18 through 21 removed outlier: 5.349A pdb=" N PHE c 18 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE c 43 " --> pdb=" O PHE c 18 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS c 20 " --> pdb=" O HIS c 41 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY c 35 " --> pdb=" O ILE c 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 93 through 94 removed outlier: 8.034A pdb=" N VAL c 94 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE c 71 " --> pdb=" O VAL c 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 125 through 127 Processing sheet with id=AA4, first strand: chain 'f' and resid 11 through 23 removed outlier: 6.566A pdb=" N LEU f 35 " --> pdb=" O VAL f 15 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL f 17 " --> pdb=" O THR f 33 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR f 33 " --> pdb=" O VAL f 17 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG f 19 " --> pdb=" O SER f 31 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER f 31 " --> pdb=" O ARG f 19 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA f 21 " --> pdb=" O ILE f 29 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE f 29 " --> pdb=" O ALA f 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 84 through 88 removed outlier: 6.383A pdb=" N ILE f 105 " --> pdb=" O ALA f 124 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N CYS f 126 " --> pdb=" O ILE f 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'g' and resid 35 through 46 removed outlier: 6.435A pdb=" N ASN g 63 " --> pdb=" O HIS g 37 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU g 39 " --> pdb=" O LEU g 61 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU g 61 " --> pdb=" O LEU g 39 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP g 41 " --> pdb=" O TYR g 59 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR g 59 " --> pdb=" O ASP g 41 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY g 43 " --> pdb=" O ALA g 57 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA g 57 " --> pdb=" O GLY g 43 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N HIS g 3 " --> pdb=" O ARG g 91 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG g 91 " --> pdb=" O HIS g 3 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU g 5 " --> pdb=" O ILE g 89 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE g 89 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL g 7 " --> pdb=" O ASN g 87 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN g 87 " --> pdb=" O VAL g 7 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU g 9 " --> pdb=" O ILE g 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 24 through 28 removed outlier: 6.168A pdb=" N THR i 59 " --> pdb=" O VAL i 51 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL i 51 " --> pdb=" O THR i 59 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR i 61 " --> pdb=" O VAL i 49 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL i 49 " --> pdb=" O THR i 61 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR i 63 " --> pdb=" O SER i 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'i' and resid 66 through 67 removed outlier: 3.739A pdb=" N LYS i 70 " --> pdb=" O PHE i 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 75 through 78 removed outlier: 5.583A pdb=" N VAL i 126 " --> pdb=" O SER i 106 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER i 106 " --> pdb=" O VAL i 126 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA i 128 " --> pdb=" O ILE i 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 40 through 45 removed outlier: 6.821A pdb=" N ILE l 33 " --> pdb=" O LEU l 41 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP l 43 " --> pdb=" O VAL l 31 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL l 31 " --> pdb=" O TRP l 43 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU l 81 " --> pdb=" O ILE l 106 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER l 108 " --> pdb=" O LEU l 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 29 through 40 removed outlier: 6.649A pdb=" N ARG m 54 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL m 37 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL m 52 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR m 39 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG m 50 " --> pdb=" O THR m 39 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N TYR m 95 " --> pdb=" O GLU m 62 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER m 64 " --> pdb=" O TYR m 95 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR m 97 " --> pdb=" O SER m 64 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR m 66 " --> pdb=" O THR m 97 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER m 78 " --> pdb=" O CYS m 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'q' and resid 50 through 51 removed outlier: 4.892A pdb=" N ILE q 19 " --> pdb=" O ILE q 36 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE q 38 " --> pdb=" O TYR q 17 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR q 17 " --> pdb=" O PHE q 38 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL q 2 " --> pdb=" O GLN q 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'r' and resid 8 through 15 removed outlier: 16.782A pdb=" N THR r 8 " --> pdb=" O ARG r 29 " (cutoff:3.500A) removed outlier: 12.917A pdb=" N ARG r 29 " --> pdb=" O THR r 8 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR r 10 " --> pdb=" O GLU r 27 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU r 27 " --> pdb=" O THR r 10 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL r 23 " --> pdb=" O VAL r 14 " (cutoff:3.500A) removed outlier: 15.857A pdb=" N LYS r 72 " --> pdb=" O SER r 42 " (cutoff:3.500A) removed outlier: 13.654A pdb=" N LYS r 44 " --> pdb=" O LYS r 72 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N TRP r 74 " --> pdb=" O LYS r 44 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N HIS r 46 " --> pdb=" O TRP r 74 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU r 76 " --> pdb=" O HIS r 46 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS r 48 " --> pdb=" O LEU r 76 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLU r 78 " --> pdb=" O HIS r 48 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS r 72 " --> pdb=" O ILE r 68 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP r 74 " --> pdb=" O ARG r 66 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ARG r 66 " --> pdb=" O TRP r 74 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N LEU r 76 " --> pdb=" O GLU r 64 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLU r 64 " --> pdb=" O LEU r 76 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU r 78 " --> pdb=" O ILE r 62 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE r 62 " --> pdb=" O GLU r 78 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL r 80 " --> pdb=" O VAL r 60 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL r 60 " --> pdb=" O VAL r 80 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 912 hydrogen bonds 1386 hydrogen bond angles 0 basepair planarities 368 basepair parallelities 597 stacking parallelities Total time for adding SS restraints: 26.97 Time building geometry restraints manager: 17.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4078 1.32 - 1.44: 15122 1.44 - 1.56: 14711 1.56 - 1.69: 2075 1.69 - 1.81: 48 Bond restraints: 36034 Sorted by residual: bond pdb=" C ASP e 192 " pdb=" N LEU e 193 " ideal model delta sigma weight residual 1.333 1.280 0.052 2.74e-02 1.33e+03 3.63e+00 bond pdb=" CA GLY f 107 " pdb=" C GLY f 107 " ideal model delta sigma weight residual 1.520 1.506 0.014 7.30e-03 1.88e+04 3.55e+00 bond pdb=" C3' C 2 99 " pdb=" C2' C 2 99 " ideal model delta sigma weight residual 1.525 1.498 0.027 1.50e-02 4.44e+03 3.29e+00 bond pdb=" N3 C 2 172 " pdb=" C4 C 2 172 " ideal model delta sigma weight residual 1.334 1.301 0.033 2.00e-02 2.50e+03 2.80e+00 bond pdb=" C8 G 2 100 " pdb=" N7 G 2 100 " ideal model delta sigma weight residual 1.305 1.272 0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 36029 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.91: 5784 105.91 - 112.95: 20856 112.95 - 120.00: 12766 120.00 - 127.04: 11899 127.04 - 134.08: 2587 Bond angle restraints: 53892 Sorted by residual: angle pdb=" C2' G 2 100 " pdb=" C1' G 2 100 " pdb=" N9 G 2 100 " ideal model delta sigma weight residual 112.00 103.64 8.36 1.50e+00 4.44e-01 3.11e+01 angle pdb=" C2' C 2 99 " pdb=" C1' C 2 99 " pdb=" N1 C 2 99 " ideal model delta sigma weight residual 114.00 107.05 6.95 1.50e+00 4.44e-01 2.15e+01 angle pdb=" C GLU f 54 " pdb=" N VAL f 55 " pdb=" CA VAL f 55 " ideal model delta sigma weight residual 120.33 123.93 -3.60 8.00e-01 1.56e+00 2.03e+01 angle pdb=" C ALA f 106 " pdb=" N GLY f 107 " pdb=" CA GLY f 107 " ideal model delta sigma weight residual 122.73 118.85 3.88 9.30e-01 1.16e+00 1.74e+01 angle pdb=" O4' G 2 612 " pdb=" C1' G 2 612 " pdb=" N9 G 2 612 " ideal model delta sigma weight residual 108.20 114.03 -5.83 1.50e+00 4.44e-01 1.51e+01 ... (remaining 53887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 20057 35.68 - 71.36: 2626 71.36 - 107.05: 270 107.05 - 142.73: 4 142.73 - 178.41: 7 Dihedral angle restraints: 22964 sinusoidal: 18678 harmonic: 4286 Sorted by residual: dihedral pdb=" O4' C 2 172 " pdb=" C1' C 2 172 " pdb=" N1 C 2 172 " pdb=" C2 C 2 172 " ideal model delta sinusoidal sigma weight residual -160.00 18.41 -178.41 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 435 " pdb=" C1' U 2 435 " pdb=" N1 U 2 435 " pdb=" C2 U 2 435 " ideal model delta sinusoidal sigma weight residual -160.00 -10.94 -149.06 1 1.50e+01 4.44e-03 7.93e+01 dihedral pdb=" O4' U 2 419 " pdb=" C1' U 2 419 " pdb=" N1 U 2 419 " pdb=" C2 U 2 419 " ideal model delta sinusoidal sigma weight residual 200.00 55.66 144.34 1 1.50e+01 4.44e-03 7.73e+01 ... (remaining 22961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 6252 0.080 - 0.161: 621 0.161 - 0.241: 42 0.241 - 0.321: 3 0.321 - 0.401: 1 Chirality restraints: 6919 Sorted by residual: chirality pdb=" C2' G 2 100 " pdb=" C3' G 2 100 " pdb=" O2' G 2 100 " pdb=" C1' G 2 100 " both_signs ideal model delta sigma weight residual False -2.75 -2.35 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1' A 2 5 " pdb=" O4' A 2 5 " pdb=" C2' A 2 5 " pdb=" N9 A 2 5 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1' A 2 294 " pdb=" O4' A 2 294 " pdb=" C2' A 2 294 " pdb=" N9 A 2 294 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 6916 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 2 99 " 0.090 2.00e-02 2.50e+03 4.64e-02 4.84e+01 pdb=" N1 C 2 99 " -0.099 2.00e-02 2.50e+03 pdb=" C2 C 2 99 " -0.018 2.00e-02 2.50e+03 pdb=" O2 C 2 99 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C 2 99 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C 2 99 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C 2 99 " 0.027 2.00e-02 2.50e+03 pdb=" C5 C 2 99 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C 2 99 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 100 " 0.087 2.00e-02 2.50e+03 3.87e-02 4.49e+01 pdb=" N9 G 2 100 " -0.097 2.00e-02 2.50e+03 pdb=" C8 G 2 100 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 2 100 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 100 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 2 100 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G 2 100 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G 2 100 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G 2 100 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 2 100 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 2 100 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G 2 100 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 612 " 0.082 2.00e-02 2.50e+03 3.48e-02 3.62e+01 pdb=" N9 G 2 612 " -0.080 2.00e-02 2.50e+03 pdb=" C8 G 2 612 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G 2 612 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G 2 612 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G 2 612 " 0.014 2.00e-02 2.50e+03 pdb=" O6 G 2 612 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G 2 612 " 0.013 2.00e-02 2.50e+03 pdb=" C2 G 2 612 " -0.008 2.00e-02 2.50e+03 pdb=" N2 G 2 612 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G 2 612 " -0.013 2.00e-02 2.50e+03 pdb=" C4 G 2 612 " -0.017 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 147 2.44 - 3.05: 19077 3.05 - 3.67: 62268 3.67 - 4.28: 98634 4.28 - 4.90: 129249 Nonbonded interactions: 309375 Sorted by model distance: nonbonded pdb=" OP1 G 41502 " pdb="MG MG 41602 " model vdw 1.825 2.170 nonbonded pdb=" OP1 C 2 573 " pdb="MG MG 21651 " model vdw 1.936 2.170 nonbonded pdb=" OP1 A 41497 " pdb="MG MG 41602 " model vdw 1.944 2.170 nonbonded pdb=" OP2 G 2 285 " pdb="MG MG 21602 " model vdw 1.948 2.170 nonbonded pdb=" OP2 U 2 557 " pdb="MG MG 21613 " model vdw 1.979 2.170 ... (remaining 309370 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=1.00 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: 3.550 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: 14.570 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 109.930 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.010 0.079 36034 Z= 0.587 Angle : 0.807 8.363 53892 Z= 0.421 Chirality : 0.049 0.401 6919 Planarity : 0.006 0.046 2984 Dihedral : 23.865 178.410 20198 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 8.22 % Allowed : 19.84 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.30 (0.18), residues: 1470 helix: -1.73 (0.18), residues: 594 sheet: -1.59 (0.29), residues: 249 loop : -2.83 (0.20), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP r 74 HIS 0.006 0.002 HIS e 42 PHE 0.020 0.002 PHE e 184 TYR 0.021 0.003 TYR m 117 ARG 0.009 0.001 ARG g 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 251 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: e 42 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7507 (p-80) REVERT: e 167 ARG cc_start: 0.5447 (tmm160) cc_final: 0.4968 (ttp-170) REVERT: f 68 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6781 (mtm-85) REVERT: g 44 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7619 (ttm-80) REVERT: g 68 GLN cc_start: 0.7820 (tp40) cc_final: 0.7419 (tp-100) REVERT: i 41 GLN cc_start: 0.8263 (tt0) cc_final: 0.8003 (tt0) REVERT: m 88 LYS cc_start: 0.8588 (tptp) cc_final: 0.8335 (ttmm) REVERT: r 20 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7857 (pttt) outliers start: 82 outliers final: 51 residues processed: 313 average time/residue: 1.6411 time to fit residues: 605.2142 Evaluate side-chains 297 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 109 PHE Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 136 SER Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 68 ARG Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain g residue 102 LEU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 55 VAL Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 66 SER Chi-restraints excluded: chain u residue 27 MET Chi-restraints excluded: chain u residue 30 THR Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 53 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 224 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 41 GLN e 128 ASN e 148 HIS e 177 HIS g 17 GLN g 52 ASN g 63 ASN i 18 GLN i 41 GLN i 42 GLN i 98 GLN l 21 HIS l 37 GLN l 49 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 46 HIS p 62 GLN q 44 GLN q 46 GLN u 6 GLN v 57 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 36034 Z= 0.160 Angle : 0.530 6.908 53892 Z= 0.281 Chirality : 0.035 0.192 6919 Planarity : 0.004 0.037 2984 Dihedral : 23.544 178.815 17915 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.11 % Allowed : 24.75 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1470 helix: 0.03 (0.21), residues: 608 sheet: -1.19 (0.31), residues: 254 loop : -2.23 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP q 60 HIS 0.002 0.001 HIS l 23 PHE 0.010 0.001 PHE e 184 TYR 0.010 0.001 TYR m 95 ARG 0.003 0.000 ARG r 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 263 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: g 68 GLN cc_start: 0.7765 (tp40) cc_final: 0.7423 (tp-100) REVERT: m 86 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7936 (ppt-90) REVERT: p 22 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7635 (m) REVERT: r 20 LYS cc_start: 0.8195 (ptpt) cc_final: 0.7819 (pttt) REVERT: s 35 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6404 (pt0) outliers start: 51 outliers final: 22 residues processed: 302 average time/residue: 1.5496 time to fit residues: 552.3341 Evaluate side-chains 275 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 250 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 242 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 0.4980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 52 ASN i 41 GLN i 42 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 35 GLN p 37 ASN p 62 GLN p 75 HIS q 46 GLN v 57 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 36034 Z= 0.323 Angle : 0.608 6.945 53892 Z= 0.316 Chirality : 0.039 0.213 6919 Planarity : 0.005 0.038 2984 Dihedral : 23.513 178.162 17856 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.11 % Allowed : 25.85 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.21), residues: 1470 helix: 0.50 (0.21), residues: 608 sheet: -0.87 (0.31), residues: 259 loop : -2.09 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP q 60 HIS 0.004 0.001 HIS e 42 PHE 0.016 0.002 PHE e 184 TYR 0.017 0.002 TYR m 117 ARG 0.005 0.001 ARG g 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 253 time to evaluate : 1.932 Fit side-chains revert: symmetry clash REVERT: e 56 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8347 (mt0) REVERT: f 53 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7116 (tpp80) REVERT: g 68 GLN cc_start: 0.7731 (tp40) cc_final: 0.7335 (tp-100) REVERT: m 43 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7825 (mtpp) REVERT: m 86 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7860 (ppt-90) REVERT: p 22 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7608 (m) REVERT: r 20 LYS cc_start: 0.8275 (ptpt) cc_final: 0.8045 (ptmt) REVERT: s 35 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6441 (pt0) outliers start: 61 outliers final: 38 residues processed: 289 average time/residue: 1.5433 time to fit residues: 524.1245 Evaluate side-chains 295 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 251 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 56 GLN Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 2.9990 chunk 168 optimal weight: 0.0980 chunk 116 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 238 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 28 GLN g 52 ASN i 41 GLN i 42 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 20 ASN p 37 ASN p 62 GLN p 75 HIS q 46 GLN v 57 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36034 Z= 0.253 Angle : 0.579 6.842 53892 Z= 0.303 Chirality : 0.037 0.210 6919 Planarity : 0.004 0.036 2984 Dihedral : 23.516 178.264 17854 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.31 % Allowed : 25.65 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.21), residues: 1470 helix: 0.76 (0.21), residues: 610 sheet: -0.73 (0.32), residues: 259 loop : -2.00 (0.22), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP q 60 HIS 0.004 0.001 HIS e 42 PHE 0.014 0.002 PHE v 37 TYR 0.016 0.002 TYR m 117 ARG 0.004 0.000 ARG f 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 255 time to evaluate : 1.996 Fit side-chains revert: symmetry clash REVERT: e 56 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: f 53 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7099 (tpp80) REVERT: g 31 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: g 68 GLN cc_start: 0.7724 (tp40) cc_final: 0.7329 (tp-100) REVERT: m 43 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7795 (mtpp) REVERT: m 86 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7845 (ppt-90) REVERT: p 22 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7580 (m) REVERT: q 12 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8072 (ttmm) REVERT: r 20 LYS cc_start: 0.8304 (ptpt) cc_final: 0.8068 (ptmt) REVERT: r 40 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6879 (mtp85) REVERT: r 66 ARG cc_start: 0.8335 (ptt-90) cc_final: 0.8083 (ppt-90) REVERT: s 35 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6427 (pt0) outliers start: 63 outliers final: 39 residues processed: 297 average time/residue: 1.5866 time to fit residues: 553.2041 Evaluate side-chains 301 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 253 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 56 GLN Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 12 LYS Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 0.0980 chunk 98 optimal weight: 6.9990 chunk 203 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 52 ASN i 41 GLN i 42 GLN i 98 GLN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 37 ASN p 62 GLN p 75 HIS q 46 GLN v 57 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36034 Z= 0.226 Angle : 0.557 6.821 53892 Z= 0.292 Chirality : 0.036 0.207 6919 Planarity : 0.004 0.034 2984 Dihedral : 23.484 178.375 17854 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.21 % Allowed : 25.95 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.22), residues: 1470 helix: 0.95 (0.21), residues: 611 sheet: -0.61 (0.33), residues: 259 loop : -1.88 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP q 60 HIS 0.004 0.001 HIS e 42 PHE 0.015 0.002 PHE v 37 TYR 0.014 0.001 TYR m 117 ARG 0.004 0.000 ARG g 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 256 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: g 31 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6333 (tt0) REVERT: g 68 GLN cc_start: 0.7870 (tp40) cc_final: 0.7443 (tp-100) REVERT: m 43 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7803 (mtpp) REVERT: m 86 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7838 (ppt-90) REVERT: p 22 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7530 (m) REVERT: q 12 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8082 (ttmm) REVERT: q 56 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7479 (mmm160) REVERT: r 20 LYS cc_start: 0.8266 (ptpt) cc_final: 0.8031 (ptmt) REVERT: r 40 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6898 (mtp85) REVERT: r 66 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8120 (ppt-90) REVERT: s 35 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6449 (pt0) outliers start: 62 outliers final: 40 residues processed: 298 average time/residue: 1.5640 time to fit residues: 548.2306 Evaluate side-chains 302 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 253 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain f residue 42 ASN Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 12 LYS Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 56 ARG Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 66 ARG Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Chi-restraints excluded: chain u residue 4 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 0.0070 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 52 ASN i 41 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 37 ASN p 62 GLN q 46 GLN v 57 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 36034 Z= 0.317 Angle : 0.603 6.955 53892 Z= 0.313 Chirality : 0.039 0.212 6919 Planarity : 0.004 0.035 2984 Dihedral : 23.466 178.366 17854 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.71 % Allowed : 26.05 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.22), residues: 1470 helix: 0.98 (0.21), residues: 610 sheet: -0.56 (0.33), residues: 259 loop : -1.86 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP q 60 HIS 0.005 0.001 HIS e 42 PHE 0.019 0.002 PHE v 37 TYR 0.016 0.002 TYR m 117 ARG 0.003 0.000 ARG f 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 262 time to evaluate : 2.091 Fit side-chains revert: symmetry clash REVERT: f 53 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7154 (tpp80) REVERT: g 31 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6360 (tt0) REVERT: g 68 GLN cc_start: 0.7789 (tp40) cc_final: 0.7390 (tp-100) REVERT: m 43 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7839 (mtpp) REVERT: m 86 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7845 (ppt-90) REVERT: p 22 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7505 (m) REVERT: r 20 LYS cc_start: 0.8304 (ptpt) cc_final: 0.8045 (ptmt) REVERT: r 40 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6932 (mtp85) REVERT: r 66 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8154 (ppt-90) REVERT: s 35 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6442 (pt0) REVERT: u 37 SER cc_start: 0.8735 (p) cc_final: 0.8419 (m) outliers start: 67 outliers final: 42 residues processed: 302 average time/residue: 1.5754 time to fit residues: 560.9756 Evaluate side-chains 310 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 260 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 66 ARG Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Chi-restraints excluded: chain u residue 4 SER Chi-restraints excluded: chain u residue 77 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 136 optimal weight: 0.0980 chunk 174 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 177 HIS g 52 ASN i 41 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 35 GLN p 37 ASN p 62 GLN q 46 GLN v 57 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36034 Z= 0.182 Angle : 0.557 8.038 53892 Z= 0.292 Chirality : 0.035 0.206 6919 Planarity : 0.004 0.034 2984 Dihedral : 23.485 178.385 17854 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.21 % Allowed : 27.35 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.22), residues: 1470 helix: 1.22 (0.22), residues: 604 sheet: -0.53 (0.33), residues: 259 loop : -1.76 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP q 60 HIS 0.006 0.001 HIS e 42 PHE 0.022 0.002 PHE v 37 TYR 0.014 0.001 TYR m 117 ARG 0.006 0.000 ARG m 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 259 time to evaluate : 1.920 Fit side-chains revert: symmetry clash REVERT: e 117 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7365 (ttt90) REVERT: f 53 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7212 (tpp80) REVERT: g 31 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6345 (tt0) REVERT: g 68 GLN cc_start: 0.7747 (tp40) cc_final: 0.7341 (tp-100) REVERT: i 70 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7268 (ptpp) REVERT: m 43 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7772 (mtpp) REVERT: m 86 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7815 (ppt-90) REVERT: p 22 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7440 (m) REVERT: r 20 LYS cc_start: 0.8311 (ptpt) cc_final: 0.8073 (ptmt) REVERT: r 40 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6929 (mtp85) REVERT: r 66 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8134 (ppt-90) REVERT: s 35 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6470 (pt0) REVERT: u 37 SER cc_start: 0.8715 (p) cc_final: 0.8403 (m) outliers start: 62 outliers final: 42 residues processed: 296 average time/residue: 1.5760 time to fit residues: 548.0027 Evaluate side-chains 310 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 258 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 117 ARG Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 70 LYS Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 66 ARG Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Chi-restraints excluded: chain u residue 4 SER Chi-restraints excluded: chain u residue 27 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 216 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 52 ASN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 35 GLN p 37 ASN p 62 GLN q 46 GLN v 57 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 36034 Z= 0.455 Angle : 0.697 8.237 53892 Z= 0.356 Chirality : 0.044 0.232 6919 Planarity : 0.005 0.043 2984 Dihedral : 23.537 179.121 17854 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 7.01 % Allowed : 26.75 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.21), residues: 1470 helix: 0.88 (0.21), residues: 611 sheet: -0.49 (0.33), residues: 254 loop : -1.88 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP l 43 HIS 0.007 0.001 HIS e 42 PHE 0.022 0.003 PHE v 37 TYR 0.019 0.002 TYR v 38 ARG 0.005 0.001 ARG m 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 256 time to evaluate : 1.958 Fit side-chains revert: symmetry clash REVERT: f 53 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7202 (tpp80) REVERT: g 31 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6379 (tt0) REVERT: g 68 GLN cc_start: 0.7830 (tp40) cc_final: 0.7450 (tp-100) REVERT: m 43 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7921 (mtpp) REVERT: m 86 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7883 (ppt-90) REVERT: p 22 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7532 (m) REVERT: r 20 LYS cc_start: 0.8269 (ptpt) cc_final: 0.8022 (ptmt) REVERT: r 40 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6952 (mtp85) REVERT: s 35 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6471 (pt0) REVERT: u 37 SER cc_start: 0.8750 (p) cc_final: 0.8439 (m) outliers start: 70 outliers final: 46 residues processed: 302 average time/residue: 1.5660 time to fit residues: 555.8647 Evaluate side-chains 307 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 75 ASP Chi-restraints excluded: chain l residue 78 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Chi-restraints excluded: chain u residue 27 MET Chi-restraints excluded: chain u residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 0.9990 chunk 208 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 177 HIS g 52 ASN i 41 GLN i 42 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 35 GLN p 37 ASN p 62 GLN q 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 36034 Z= 0.182 Angle : 0.569 8.732 53892 Z= 0.299 Chirality : 0.036 0.276 6919 Planarity : 0.004 0.035 2984 Dihedral : 23.559 178.366 17854 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.01 % Allowed : 28.86 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.22), residues: 1470 helix: 1.20 (0.22), residues: 605 sheet: -0.53 (0.33), residues: 259 loop : -1.72 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP q 60 HIS 0.005 0.001 HIS e 42 PHE 0.023 0.002 PHE v 37 TYR 0.014 0.001 TYR m 117 ARG 0.002 0.000 ARG u 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 257 time to evaluate : 1.918 Fit side-chains revert: symmetry clash REVERT: f 53 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7239 (tpp80) REVERT: g 31 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6325 (tt0) REVERT: g 68 GLN cc_start: 0.7931 (tp40) cc_final: 0.7513 (tp-100) REVERT: m 86 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8040 (ppt-90) REVERT: r 20 LYS cc_start: 0.8268 (ptpt) cc_final: 0.8017 (ptmt) REVERT: s 35 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6451 (pt0) REVERT: u 37 SER cc_start: 0.8708 (p) cc_final: 0.8408 (m) outliers start: 50 outliers final: 36 residues processed: 290 average time/residue: 1.6131 time to fit residues: 547.6346 Evaluate side-chains 293 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 253 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain f residue 53 ARG Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 6 VAL Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 163 optimal weight: 0.1980 chunk 246 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 195 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 208 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 177 HIS g 52 ASN i 42 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 35 GLN p 62 GLN q 46 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36034 Z= 0.211 Angle : 0.557 8.844 53892 Z= 0.292 Chirality : 0.036 0.205 6919 Planarity : 0.004 0.034 2984 Dihedral : 23.443 178.261 17852 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.21 % Allowed : 29.46 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.22), residues: 1470 helix: 1.33 (0.22), residues: 604 sheet: -0.48 (0.34), residues: 259 loop : -1.67 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 60 HIS 0.005 0.001 HIS e 42 PHE 0.023 0.002 PHE v 37 TYR 0.014 0.002 TYR m 117 ARG 0.006 0.000 ARG g 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 258 time to evaluate : 1.908 Fit side-chains revert: symmetry clash REVERT: g 31 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6340 (tt0) REVERT: g 68 GLN cc_start: 0.7902 (tp40) cc_final: 0.7468 (tp-100) REVERT: i 70 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7243 (ptpp) REVERT: m 86 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8011 (ppt-90) REVERT: r 20 LYS cc_start: 0.8324 (ptpt) cc_final: 0.8047 (ptmt) REVERT: s 35 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6450 (pt0) REVERT: u 37 SER cc_start: 0.8716 (p) cc_final: 0.8449 (m) outliers start: 42 outliers final: 35 residues processed: 284 average time/residue: 1.6641 time to fit residues: 554.8059 Evaluate side-chains 292 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 253 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 109 PHE Chi-restraints excluded: chain e residue 111 SER Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 155 LEU Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 161 GLU Chi-restraints excluded: chain g residue 31 GLU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 98 GLU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 70 LYS Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain l residue 41 LEU Chi-restraints excluded: chain l residue 94 SER Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 47 SER Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 86 ARG Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 54 ARG Chi-restraints excluded: chain q residue 24 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 8 THR Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 35 GLU Chi-restraints excluded: chain s residue 45 THR Chi-restraints excluded: chain u residue 4 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 201 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 91 ASN e 177 HIS g 52 ASN i 42 GLN i 98 GLN l 107 ASN ** l 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 111 ASN p 20 ASN p 35 GLN p 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102712 restraints weight = 39256.785| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 0.40 r_work: 0.2935 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work: 0.2721 rms_B_bonded: 4.20 restraints_weight: 0.1250 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 36034 Z= 0.369 Angle : 0.637 8.889 53892 Z= 0.328 Chirality : 0.041 0.217 6919 Planarity : 0.005 0.037 2984 Dihedral : 23.463 178.082 17851 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.51 % Allowed : 29.56 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.22), residues: 1470 helix: 1.10 (0.21), residues: 611 sheet: -0.41 (0.34), residues: 254 loop : -1.75 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP q 60 HIS 0.006 0.001 HIS e 42 PHE 0.024 0.002 PHE v 37 TYR 0.017 0.002 TYR m 117 ARG 0.004 0.001 ARG p 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9980.80 seconds wall clock time: 178 minutes 13.32 seconds (10693.32 seconds total)