Starting phenix.real_space_refine on Thu Feb 22 06:03:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/02_2024/6ypu_10869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/02_2024/6ypu_10869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/02_2024/6ypu_10869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/02_2024/6ypu_10869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/02_2024/6ypu_10869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ypu_10869/02_2024/6ypu_10869_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1040 5.49 5 Mg 59 5.21 5 S 28 5.16 5 C 16728 2.51 5 N 6241 2.21 5 O 9226 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 GLU 52": "OE1" <-> "OE2" Residue "e GLU 59": "OE1" <-> "OE2" Residue "e TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "e ARG 123": "NH1" <-> "NH2" Residue "e ARG 131": "NH1" <-> "NH2" Residue "e ASP 143": "OD1" <-> "OD2" Residue "e GLU 149": "OE1" <-> "OE2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "e ASP 176": "OD1" <-> "OD2" Residue "e GLU 181": "OE1" <-> "OE2" Residue "e ARG 190": "NH1" <-> "NH2" Residue "e GLU 199": "OE1" <-> "OE2" Residue "e TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 12": "OE1" <-> "OE2" Residue "f ASP 18": "OD1" <-> "OD2" Residue "f PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 49": "NH1" <-> "NH2" Residue "f GLU 64": "OE1" <-> "OE2" Residue "f TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 100": "OE1" <-> "OE2" Residue "g ASP 16": "OD1" <-> "OD2" Residue "g GLU 23": "OE1" <-> "OE2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g ASP 41": "OD1" <-> "OD2" Residue "g TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 76": "OE1" <-> "OE2" Residue "g ASP 82": "OD1" <-> "OD2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "i ASP 9": "OD1" <-> "OD2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 68": "OE1" <-> "OE2" Residue "i GLU 74": "OE1" <-> "OE2" Residue "i GLU 125": "OE1" <-> "OE2" Residue "l PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 67": "OE1" <-> "OE2" Residue "l ASP 75": "OD1" <-> "OD2" Residue "l GLU 93": "OE1" <-> "OE2" Residue "m GLU 17": "OE1" <-> "OE2" Residue "m TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 10": "OE1" <-> "OE2" Residue "p PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 38": "OD1" <-> "OD2" Residue "q PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 28": "NH1" <-> "NH2" Residue "q ASP 29": "OD1" <-> "OD2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "q ASP 55": "OD1" <-> "OD2" Residue "q PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 72": "OD1" <-> "OD2" 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 GLU 49": "OE1" <-> "OE2" Residue "u ASP 63": "OD1" <-> "OD2" Residue "v PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 39": "OE1" <-> "OE2" Residue "v TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33322 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': 72, 'rna2p_pyr': 41, 'rna3p_pur': 457, 'rna3p_pyr': 324} Link IDs: {'rna2p': 113, 'rna3p': 780} 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Unusual residues: {' MG': 53} Classifications: {'undetermined': 53} Link IDs: {None: 52} Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 46 Unusual residues: {' MG': 6, 'AKN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 17.34, per 1000 atoms: 0.52 Number of scatterers: 33322 At special positions: 0 Unit cell: (206.51, 159.43, 153.01, 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 59 11.99 O 9226 8.00 N 6241 7.00 C 16728 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: 17.34 Conformation dependent library (CDL) restraints added in 2.5 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... running ksdssp... Secondary structure from input PDB file: 51 helices and 13 sheets defined 35.4% alpha, 15.4% beta 331 base pairs and 588 stacking pairs defined. Time for finding SS restraints: 22.22 Creating SS restraints... Processing helix chain 'c' and resid 27 through 29 No H-bonds generated for 'chain 'c' and resid 27 through 29' Processing helix chain 'c' and resid 45 through 63 Proline residue: c 50 - end of helix removed outlier: 3.752A pdb=" N ASN c 53 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP c 54 " --> pdb=" O PRO c 50 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE c 58 " --> pdb=" O ASP c 54 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA c 59 " --> pdb=" O ALA c 55 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN c 60 " --> pdb=" O LEU c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 87 removed outlier: 4.392A pdb=" N GLU c 84 " --> pdb=" O ASN c 80 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA c 86 " --> pdb=" O ILE c 82 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN c 87 " --> pdb=" O ARG c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 121 removed outlier: 4.704A pdb=" N GLN c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER c 112 " --> pdb=" O THR c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 133 through 148 Processing helix chain 'c' and resid 151 through 153 No H-bonds generated for 'chain 'c' and resid 151 through 153' Processing helix chain 'c' and resid 172 through 181 removed outlier: 3.688A pdb=" N GLU c 177 " --> pdb=" O ILE c 173 " (cutoff:3.500A) Processing helix chain 'c' and resid 209 through 224 Processing helix chain 'e' and resid 10 through 15 removed outlier: 3.615A pdb=" N ARG e 14 " --> pdb=" O LYS e 10 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU e 15 " --> pdb=" O LEU e 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 10 through 15' Processing helix chain 'e' and resid 54 through 67 Processing helix chain 'e' and resid 71 through 81 Processing helix chain 'e' and resid 88 through 97 removed outlier: 3.634A pdb=" N LEU e 92 " --> pdb=" O THR e 88 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU e 93 " --> pdb=" O GLY e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 100 through 106 Processing helix chain 'e' and resid 113 through 121 removed outlier: 4.267A pdb=" N GLN e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 129 No H-bonds generated for 'chain 'e' and resid 127 through 129' Processing helix chain 'e' and resid 149 through 151 No H-bonds generated for 'chain 'e' and resid 149 through 151' Processing helix chain 'e' and resid 156 through 164 removed outlier: 3.952A pdb=" N ALA e 160 " --> pdb=" O ARG e 156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU e 162 " --> pdb=" O LYS e 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 207 removed outlier: 3.904A pdb=" N GLU e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER e 207 " --> pdb=" O VAL e 203 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 67 Processing helix chain 'f' and resid 108 through 115 removed outlier: 3.745A pdb=" N ALA f 112 " --> pdb=" O ALA f 109 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU f 115 " --> pdb=" O ALA f 112 " (cutoff:3.500A) Processing helix chain 'f' and resid 132 through 144 Processing helix chain 'f' and resid 149 through 155 removed outlier: 4.022A pdb=" N ALA f 153 " --> pdb=" O PRO f 149 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 14 No H-bonds generated for 'chain 'g' and resid 12 through 14' Processing helix chain 'g' and resid 19 through 31 removed outlier: 4.155A pdb=" N ARG g 24 " --> pdb=" O GLY g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 79 Processing helix chain 'i' and resid 7 through 20 Processing helix chain 'i' and resid 31 through 42 Processing helix chain 'i' and resid 96 through 99 Processing helix chain 'i' and resid 114 through 120 removed outlier: 3.646A pdb=" N ALA i 119 " --> pdb=" O ARG i 115 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA i 120 " --> pdb=" O ALA i 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 56 Processing helix chain 'l' and resid 59 through 76 removed outlier: 4.145A pdb=" N ASP l 75 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 90 through 100 removed outlier: 4.125A pdb=" N GLU l 93 " --> pdb=" O PRO l 90 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER l 94 " --> pdb=" O GLY l 91 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA l 95 " --> pdb=" O ARG l 92 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 9 Processing helix chain 'm' and resid 114 through 116 No H-bonds generated for 'chain 'm' and resid 114 through 116' Processing helix chain 'p' and resid 5 through 15 removed outlier: 3.505A pdb=" N ILE p 12 " --> pdb=" O ARG p 8 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS p 14 " --> pdb=" O GLU p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 25 through 45 removed outlier: 3.795A pdb=" N GLN p 40 " --> pdb=" O ILE p 36 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY p 41 " --> pdb=" O ASN p 37 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N HIS p 42 " --> pdb=" O ASP p 38 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA p 45 " --> pdb=" O GLY p 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 73 removed outlier: 3.712A pdb=" N LYS p 65 " --> pdb=" O ASN p 61 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY p 72 " --> pdb=" O ASP p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 85 Processing helix chain 'q' and resid 54 through 63 Processing helix chain 'q' and resid 71 through 77 removed outlier: 3.557A pdb=" N ALA q 76 " --> pdb=" O ALA q 72 " (cutoff:3.500A) Processing helix chain 's' and resid 26 through 28 No H-bonds generated for 'chain 's' and resid 26 through 28' Processing helix chain 's' and resid 30 through 32 No H-bonds generated for 'chain 's' and resid 30 through 32' Processing helix chain 's' and resid 42 through 45 No H-bonds generated for 'chain 's' and resid 42 through 45' Processing helix chain 's' and resid 49 through 65 removed outlier: 3.583A pdb=" N ARG s 53 " --> pdb=" O ALA s 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN s 54 " --> pdb=" O ARG s 50 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR s 64 " --> pdb=" O LYS s 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 5 through 41 removed outlier: 3.634A pdb=" N LYS u 16 " --> pdb=" O ARG u 12 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER u 23 " --> pdb=" O LYS u 19 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU u 24 " --> pdb=" O HIS u 20 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY u 41 " --> pdb=" O SER u 37 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 51 Processing helix chain 'u' and resid 55 through 63 Processing helix chain 'u' and resid 69 through 80 Processing helix chain 'v' and resid 12 through 25 removed outlier: 3.982A pdb=" N ILE v 16 " --> pdb=" O VAL v 12 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG v 17 " --> pdb=" O ASP v 13 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG v 18 " --> pdb=" O VAL v 14 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG v 21 " --> pdb=" O ARG v 17 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU v 24 " --> pdb=" O LYS v 20 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS v 25 " --> pdb=" O ARG v 21 " (cutoff:3.500A) Processing helix chain 'v' and resid 30 through 33 No H-bonds generated for 'chain 'v' and resid 30 through 33' Processing helix chain 'v' and resid 41 through 57 removed outlier: 3.526A pdb=" N ALA v 50 " --> pdb=" O LYS v 46 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN v 57 " --> pdb=" O VAL v 53 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'c' and resid 70 through 72 removed outlier: 8.004A pdb=" N VAL c 165 " --> pdb=" O PRO c 184 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE c 186 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR c 200 " --> pdb=" O GLY c 187 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL c 189 " --> pdb=" O TYR c 200 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE c 202 " --> pdb=" O VAL c 189 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'f' and resid 45 through 52 removed outlier: 6.632A pdb=" N VAL f 37 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU f 14 " --> pdb=" O VAL f 37 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY f 39 " --> pdb=" O GLU f 12 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU f 12 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'f' and resid 84 through 88 Processing sheet with id= D, first strand: chain 'g' and resid 44 through 46 removed outlier: 3.734A pdb=" N ILE g 6 " --> pdb=" O MET g 62 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HIS g 3 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG g 86 " --> pdb=" O LEU g 9 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N HIS g 11 " --> pdb=" O ILE g 84 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE g 84 " --> pdb=" O HIS g 11 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'g' and resid 35 through 39 removed outlier: 6.694A pdb=" N ASN g 63 " --> pdb=" O HIS g 37 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.772A pdb=" N ASN i 48 " --> pdb=" O THR i 63 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'i' and resid 76 through 78 removed outlier: 6.787A pdb=" N ILE i 104 " --> pdb=" O ILE i 127 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE i 129 " --> pdb=" O ILE i 102 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE i 102 " --> pdb=" O PHE i 129 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'l' and resid 40 through 45 removed outlier: 6.966A pdb=" N ILE l 33 " --> pdb=" O LEU l 41 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP l 43 " --> pdb=" O VAL l 31 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL l 31 " --> pdb=" O TRP l 43 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR l 45 " --> pdb=" O THR l 29 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR l 29 " --> pdb=" O THR l 45 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN l 80 " --> pdb=" O GLY l 18 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA l 20 " --> pdb=" O ASN l 80 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP l 82 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE l 22 " --> pdb=" O ASP l 82 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU l 84 " --> pdb=" O ILE l 22 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA l 24 " --> pdb=" O LEU l 84 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS l 86 " --> pdb=" O ALA l 24 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'm' and resid 95 through 97 removed outlier: 6.379A pdb=" N ARG m 54 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL m 37 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL m 52 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR m 39 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG m 50 " --> pdb=" O THR m 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'q' and resid 2 through 8 Processing sheet with id= K, first strand: chain 'q' and resid 37 through 39 Processing sheet with id= L, first strand: chain 'r' and resid 74 through 76 removed outlier: 16.880A pdb=" N THR r 8 " --> pdb=" O ARG r 29 " (cutoff:3.500A) removed outlier: 13.372A pdb=" N ARG r 29 " --> pdb=" O THR r 8 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR r 10 " --> pdb=" O GLU r 27 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU r 27 " --> pdb=" O THR r 10 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL r 23 " --> pdb=" O VAL r 14 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'r' and resid 59 through 61 removed outlier: 3.940A pdb=" N VAL r 59 " --> pdb=" O GLU r 81 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU r 81 " --> pdb=" O VAL r 59 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR r 61 " --> pdb=" O VAL r 79 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL r 79 " --> pdb=" O THR r 61 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 397 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 832 hydrogen bonds 1280 hydrogen bond angles 0 basepair planarities 331 basepair parallelities 588 stacking parallelities Total time for adding SS restraints: 32.41 Time building geometry restraints manager: 18.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3407 1.30 - 1.43: 15692 1.43 - 1.56: 14854 1.56 - 1.68: 2075 1.68 - 1.81: 48 Bond restraints: 36076 Sorted by residual: bond pdb=" C35 AKN 41607 " pdb=" N12 AKN 41607 " ideal model delta sigma weight residual 1.339 1.471 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C24 AKN 41607 " pdb=" C26 AKN 41607 " ideal model delta sigma weight residual 1.532 1.450 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C7 AKN 41607 " pdb=" O8 AKN 41607 " ideal model delta sigma weight residual 1.420 1.496 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C28 AKN 41607 " pdb=" O29 AKN 41607 " ideal model delta sigma weight residual 1.421 1.491 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 AKN 41607 " pdb=" C5 AKN 41607 " ideal model delta sigma weight residual 1.525 1.457 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 36071 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.19: 5114 105.19 - 112.47: 20281 112.47 - 119.75: 13205 119.75 - 127.03: 12696 127.03 - 134.32: 2657 Bond angle restraints: 53953 Sorted by residual: angle pdb=" N TYR e 53 " pdb=" CA TYR e 53 " pdb=" C TYR e 53 " ideal model delta sigma weight residual 114.56 106.68 7.88 1.27e+00 6.20e-01 3.85e+01 angle pdb=" N VAL r 14 " pdb=" CA VAL r 14 " pdb=" C VAL r 14 " ideal model delta sigma weight residual 113.71 109.26 4.45 9.50e-01 1.11e+00 2.20e+01 angle pdb=" O4' G 2 612 " pdb=" C1' G 2 612 " pdb=" N9 G 2 612 " ideal model delta sigma weight residual 108.20 114.93 -6.73 1.50e+00 4.44e-01 2.01e+01 angle pdb=" C2' A 2 360 " pdb=" C1' A 2 360 " pdb=" N9 A 2 360 " ideal model delta sigma weight residual 112.00 118.14 -6.14 1.50e+00 4.44e-01 1.67e+01 angle pdb=" O3' G 2 186 " pdb=" C3' G 2 186 " pdb=" C2' G 2 186 " ideal model delta sigma weight residual 113.70 119.35 -5.65 1.50e+00 4.44e-01 1.42e+01 ... (remaining 53948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 20342 35.76 - 71.53: 2433 71.53 - 107.29: 252 107.29 - 143.05: 7 143.05 - 178.82: 11 Dihedral angle restraints: 23045 sinusoidal: 18759 harmonic: 4286 Sorted by residual: dihedral pdb=" O4' C 2 131 " pdb=" C1' C 2 131 " pdb=" N1 C 2 131 " pdb=" C2 C 2 131 " ideal model delta sinusoidal sigma weight residual -160.00 18.82 -178.82 1 1.50e+01 4.44e-03 8.53e+01 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 200.00 24.73 175.27 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 2 463 " pdb=" C1' U 2 463 " pdb=" N1 U 2 463 " pdb=" C2 U 2 463 " ideal model delta sinusoidal sigma weight residual -160.00 14.91 -174.91 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 23042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5698 0.072 - 0.145: 1095 0.145 - 0.217: 123 0.217 - 0.290: 15 0.290 - 0.362: 4 Chirality restraints: 6935 Sorted by residual: chirality pdb=" C1' U 2 361 " pdb=" O4' U 2 361 " pdb=" C2' U 2 361 " pdb=" N1 U 2 361 " both_signs ideal model delta sigma weight residual False 2.47 2.10 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C3' G 2 186 " pdb=" C4' G 2 186 " pdb=" O3' G 2 186 " pdb=" C2' G 2 186 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1' G 41527 " pdb=" O4' G 41527 " pdb=" C2' G 41527 " pdb=" N9 G 41527 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 6932 not shown) Planarity restraints: 2985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 612 " 0.066 2.00e-02 2.50e+03 2.81e-02 2.38e+01 pdb=" N9 G 2 612 " -0.066 2.00e-02 2.50e+03 pdb=" C8 G 2 612 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G 2 612 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G 2 612 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 612 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G 2 612 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G 2 612 " 0.008 2.00e-02 2.50e+03 pdb=" C2 G 2 612 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G 2 612 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 2 612 " -0.015 2.00e-02 2.50e+03 pdb=" C4 G 2 612 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 360 " -0.060 2.00e-02 2.50e+03 2.82e-02 2.19e+01 pdb=" N9 A 2 360 " 0.059 2.00e-02 2.50e+03 pdb=" C8 A 2 360 " 0.013 2.00e-02 2.50e+03 pdb=" N7 A 2 360 " -0.017 2.00e-02 2.50e+03 pdb=" C5 A 2 360 " 0.019 2.00e-02 2.50e+03 pdb=" C6 A 2 360 " -0.020 2.00e-02 2.50e+03 pdb=" N6 A 2 360 " -0.015 2.00e-02 2.50e+03 pdb=" N1 A 2 360 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A 2 360 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A 2 360 " -0.000 2.00e-02 2.50e+03 pdb=" C4 A 2 360 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 331 " 0.055 2.00e-02 2.50e+03 2.97e-02 1.99e+01 pdb=" N1 C 2 331 " -0.068 2.00e-02 2.50e+03 pdb=" C2 C 2 331 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C 2 331 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C 2 331 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C 2 331 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C 2 331 " 0.014 2.00e-02 2.50e+03 pdb=" C5 C 2 331 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C 2 331 " -0.008 2.00e-02 2.50e+03 ... (remaining 2982 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 124 2.46 - 3.07: 19319 3.07 - 3.68: 57233 3.68 - 4.29: 94385 4.29 - 4.90: 125258 Nonbonded interactions: 296319 Sorted by model distance: nonbonded pdb=" OP1 G 41502 " pdb="MG MG 41602 " model vdw 1.849 2.170 nonbonded pdb=" OP1 A 2 530 " pdb="MG MG 21636 " model vdw 1.897 2.170 nonbonded pdb=" O2 C 2 152 " pdb=" N2 G 2 161 " model vdw 1.931 2.496 nonbonded pdb=" OP2 G 2 285 " pdb="MG MG 21602 " model vdw 2.051 2.170 nonbonded pdb=" OP2 A 2 191 " pdb="MG MG 21629 " model vdw 2.056 2.170 ... (remaining 296314 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: 3.350 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: 14.370 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 123.830 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.012 0.132 36076 Z= 0.700 Angle : 0.989 9.647 53953 Z= 0.495 Chirality : 0.057 0.362 6935 Planarity : 0.007 0.065 2985 Dihedral : 23.552 178.817 20279 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.25 % Favored : 90.54 % Rotamer: Outliers : 11.02 % Allowed : 20.24 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.96 (0.18), residues: 1470 helix: -2.40 (0.17), residues: 558 sheet: -1.23 (0.32), residues: 234 loop : -3.35 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP q 60 HIS 0.006 0.002 HIS f 120 PHE 0.021 0.003 PHE p 43 TYR 0.026 0.003 TYR m 117 ARG 0.007 0.001 ARG l 127 *********************** 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 309 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 199 time to evaluate : 1.980 Fit side-chains revert: symmetry clash REVERT: e 41 GLN cc_start: 0.7417 (tt0) cc_final: 0.7170 (tt0) REVERT: e 72 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7919 (ttt180) REVERT: f 14 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8469 (tt) REVERT: g 92 ARG cc_start: 0.8270 (mmt180) cc_final: 0.7930 (mmt180) REVERT: l 33 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8331 (mm) REVERT: p 58 ARG cc_start: 0.8467 (ttm170) cc_final: 0.8212 (ttp-170) REVERT: p 71 ASN cc_start: 0.8955 (t0) cc_final: 0.8733 (t0) REVERT: r 29 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7586 (ttm110) REVERT: v 54 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7863 (tttt) outliers start: 110 outliers final: 82 residues processed: 295 average time/residue: 1.4741 time to fit residues: 516.9548 Evaluate side-chains 269 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 184 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 13 ARG Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 72 ARG Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 121 SER Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 136 SER Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 197 ILE Chi-restraints excluded: chain e residue 200 SER Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 31 SER Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 159 SER Chi-restraints excluded: chain f residue 162 GLU Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 65 GLU Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain i residue 80 SER Chi-restraints excluded: chain i residue 95 SER Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain i residue 108 SER Chi-restraints excluded: chain i residue 131 SER Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 84 LEU Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 108 SER Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 12 ARG 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 41 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 59 SER Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 77 SER Chi-restraints excluded: chain v residue 55 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 126 optimal weight: 0.0970 chunk 100 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 117 optimal weight: 0.0670 chunk 144 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 GLN e 122 HIS e 177 HIS f 120 HIS f 137 ASN g 3 HIS g 58 HIS g 63 ASN i 16 ASN i 42 GLN l 49 GLN l 63 GLN m 96 HIS m 111 ASN p 42 HIS p 62 GLN q 26 ASN q 44 GLN r 32 HIS s 52 GLN u 13 GLN u 68 HIS u 70 ASN u 75 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 36076 Z= 0.124 Angle : 0.529 7.971 53953 Z= 0.277 Chirality : 0.035 0.224 6935 Planarity : 0.004 0.052 2985 Dihedral : 23.072 175.887 18049 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.91 % Allowed : 26.25 % Favored : 68.84 % 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: -2.22 (0.21), residues: 1470 helix: -0.49 (0.22), residues: 544 sheet: -0.67 (0.32), residues: 241 loop : -2.65 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 60 HIS 0.004 0.001 HIS r 32 PHE 0.011 0.001 PHE e 184 TYR 0.012 0.001 TYR m 117 ARG 0.009 0.000 ARG m 86 *********************** 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 245 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 196 time to evaluate : 2.152 Fit side-chains REVERT: g 91 ARG cc_start: 0.8033 (ttt-90) cc_final: 0.7794 (ttp-170) REVERT: i 70 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7476 (mtmm) REVERT: l 17 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6122 (mp0) REVERT: p 58 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7930 (ttp-170) REVERT: p 61 ASN cc_start: 0.7852 (p0) cc_final: 0.7379 (m110) REVERT: q 1 MET cc_start: 0.7904 (ttm) cc_final: 0.7666 (ttm) REVERT: r 29 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.7113 (ttm110) outliers start: 49 outliers final: 22 residues processed: 233 average time/residue: 1.5952 time to fit residues: 436.1478 Evaluate side-chains 200 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 49 ASP Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain u residue 37 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 222 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 GLN g 63 ASN i 42 GLN i 53 GLN l 27 ASN p 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 36076 Z= 0.416 Angle : 0.728 8.344 53953 Z= 0.367 Chirality : 0.045 0.270 6935 Planarity : 0.006 0.058 2985 Dihedral : 23.141 179.250 17944 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.41 % Favored : 92.52 % Rotamer: Outliers : 7.82 % Allowed : 25.75 % 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: -2.05 (0.21), residues: 1470 helix: -0.36 (0.22), residues: 553 sheet: -0.47 (0.33), residues: 234 loop : -2.59 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP q 60 HIS 0.005 0.001 HIS p 48 PHE 0.017 0.002 PHE f 140 TYR 0.024 0.002 TYR m 117 ARG 0.005 0.001 ARG m 86 *********************** 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 264 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 186 time to evaluate : 2.269 Fit side-chains REVERT: e 204 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: f 35 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8982 (tp) REVERT: g 91 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.7957 (ttp-170) REVERT: g 92 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7897 (mmt90) REVERT: i 70 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7547 (mtmm) REVERT: l 82 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5857 (m-30) REVERT: l 111 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7483 (t0) REVERT: q 1 MET cc_start: 0.7969 (ttm) cc_final: 0.7693 (ttm) REVERT: r 29 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.7206 (ttm110) REVERT: r 40 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7079 (mtm-85) REVERT: s 31 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7856 (mt0) outliers start: 78 outliers final: 41 residues processed: 243 average time/residue: 1.4321 time to fit residues: 415.5293 Evaluate side-chains 229 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 181 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain f residue 25 LYS Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 79 THR Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 0.0570 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN l 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36076 Z= 0.220 Angle : 0.598 8.214 53953 Z= 0.312 Chirality : 0.039 0.254 6935 Planarity : 0.005 0.054 2985 Dihedral : 23.119 179.824 17941 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 7.11 % Allowed : 27.05 % Favored : 65.83 % 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: -1.70 (0.21), residues: 1470 helix: -0.02 (0.23), residues: 551 sheet: -0.33 (0.33), residues: 239 loop : -2.43 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 60 HIS 0.004 0.001 HIS e 42 PHE 0.015 0.001 PHE f 140 TYR 0.017 0.002 TYR m 117 ARG 0.004 0.000 ARG g 79 *********************** 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 248 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 177 time to evaluate : 2.100 Fit side-chains REVERT: e 33 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6394 (tptt) REVERT: e 193 LEU cc_start: 0.5465 (OUTLIER) cc_final: 0.4793 (mt) REVERT: e 204 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6684 (mt-10) REVERT: g 91 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7960 (ttp-170) REVERT: i 70 LYS cc_start: 0.7735 (mtmm) cc_final: 0.7533 (mtmm) REVERT: l 33 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7965 (mm) REVERT: l 111 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7435 (t0) REVERT: r 29 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7100 (ttm110) outliers start: 71 outliers final: 41 residues processed: 231 average time/residue: 1.4415 time to fit residues: 397.4431 Evaluate side-chains 219 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 172 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 77 LEU Chi-restraints excluded: chain g residue 91 ARG Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 111 ASP 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 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain v residue 42 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: 0.0970 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 0.2980 chunk 214 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36076 Z= 0.225 Angle : 0.582 8.050 53953 Z= 0.302 Chirality : 0.038 0.243 6935 Planarity : 0.004 0.054 2985 Dihedral : 23.039 179.558 17939 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 7.72 % Allowed : 25.85 % 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: -1.41 (0.22), residues: 1470 helix: 0.27 (0.23), residues: 551 sheet: -0.17 (0.33), residues: 239 loop : -2.31 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP q 60 HIS 0.004 0.001 HIS m 96 PHE 0.014 0.001 PHE f 140 TYR 0.016 0.001 TYR m 117 ARG 0.007 0.000 ARG g 79 *********************** 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 253 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 176 time to evaluate : 1.966 Fit side-chains REVERT: e 33 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6395 (tptt) REVERT: e 158 LYS cc_start: 0.4748 (OUTLIER) cc_final: 0.4463 (tmtt) REVERT: e 193 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.4758 (mt) REVERT: e 204 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: f 35 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8904 (tp) REVERT: g 35 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6907 (mt0) REVERT: g 44 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7244 (ptt180) REVERT: g 91 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7947 (ttp-170) REVERT: l 17 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6143 (mp0) REVERT: l 33 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7957 (mm) REVERT: l 111 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7404 (t0) REVERT: r 29 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.7094 (ttm110) REVERT: r 40 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7030 (mtm-85) outliers start: 77 outliers final: 45 residues processed: 232 average time/residue: 1.5210 time to fit residues: 418.1527 Evaluate side-chains 228 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 171 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain e residue 205 LEU Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 35 GLN Chi-restraints excluded: chain g residue 44 ARG Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 77 LEU Chi-restraints excluded: chain g residue 91 ARG Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain l residue 17 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain v residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 36076 Z= 0.473 Angle : 0.772 9.212 53953 Z= 0.386 Chirality : 0.047 0.297 6935 Planarity : 0.006 0.058 2985 Dihedral : 23.155 179.182 17939 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.62 % Favored : 92.31 % Rotamer: Outliers : 8.82 % Allowed : 26.15 % Favored : 65.03 % 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: -1.65 (0.21), residues: 1470 helix: -0.05 (0.23), residues: 557 sheet: -0.20 (0.34), residues: 232 loop : -2.37 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP q 60 HIS 0.005 0.002 HIS g 3 PHE 0.018 0.002 PHE f 140 TYR 0.021 0.002 TYR m 117 ARG 0.006 0.001 ARG g 79 *********************** 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 269 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 181 time to evaluate : 2.154 Fit side-chains REVERT: e 33 LYS cc_start: 0.6613 (OUTLIER) cc_final: 0.5995 (mmtp) REVERT: e 61 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8389 (tp40) REVERT: e 193 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.4804 (mt) REVERT: e 204 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6833 (mt-10) REVERT: f 35 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9016 (tp) REVERT: f 100 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: g 35 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: g 46 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: g 91 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7954 (ttp-170) REVERT: l 111 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7655 (t0) REVERT: q 1 MET cc_start: 0.7970 (ttm) cc_final: 0.7723 (ttm) REVERT: r 29 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.7183 (ttm110) REVERT: r 40 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7020 (mtm-85) REVERT: s 31 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7878 (mt0) outliers start: 88 outliers final: 55 residues processed: 246 average time/residue: 1.4273 time to fit residues: 419.8050 Evaluate side-chains 244 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 178 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 41 GLN Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 193 LEU Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 100 GLU Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 159 SER Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 35 GLN Chi-restraints excluded: chain g residue 46 GLN Chi-restraints excluded: chain g residue 56 LYS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 77 LEU Chi-restraints excluded: chain g residue 91 ARG Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 106 ILE Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 118 ASN Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 21 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 44 LYS Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 40 ARG Chi-restraints excluded: chain r residue 43 THR Chi-restraints excluded: chain s residue 31 GLN Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain v residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 135 optimal weight: 0.1980 chunk 201 optimal weight: 0.5980 chunk 133 optimal weight: 0.0060 chunk 238 optimal weight: 0.4980 chunk 148 optimal weight: 0.0010 chunk 145 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 154 GLN g 63 ASN i 42 GLN i 53 GLN l 27 ASN u 20 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 36076 Z= 0.114 Angle : 0.521 8.078 53953 Z= 0.272 Chirality : 0.034 0.214 6935 Planarity : 0.004 0.053 2985 Dihedral : 22.928 179.027 17939 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.31 % Allowed : 28.46 % Favored : 65.23 % 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: -1.04 (0.22), residues: 1470 helix: 0.58 (0.24), residues: 555 sheet: 0.06 (0.34), residues: 234 loop : -2.11 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP q 60 HIS 0.003 0.001 HIS e 42 PHE 0.012 0.001 PHE f 140 TYR 0.011 0.001 TYR m 117 ARG 0.006 0.000 ARG g 79 *********************** 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 249 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 186 time to evaluate : 2.110 Fit side-chains REVERT: e 33 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6349 (tptt) REVERT: e 204 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6749 (mt-10) REVERT: p 61 ASN cc_start: 0.7781 (p0) cc_final: 0.7458 (m110) REVERT: q 1 MET cc_start: 0.7866 (ttm) cc_final: 0.7576 (ttm) outliers start: 63 outliers final: 40 residues processed: 234 average time/residue: 1.5735 time to fit residues: 435.7917 Evaluate side-chains 216 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 130 ARG Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 26 ILE Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 102 VAL Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 12 ARG 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 41 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 46 VAL Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain v residue 42 THR 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: 6.9990 chunk 142 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 151 optimal weight: 0.0770 chunk 162 optimal weight: 0.0770 chunk 117 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 216 optimal weight: 0.0980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 20 GLN ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 35 GLN p 40 GLN q 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36076 Z= 0.138 Angle : 0.500 8.332 53953 Z= 0.260 Chirality : 0.033 0.216 6935 Planarity : 0.004 0.050 2985 Dihedral : 22.863 179.528 17939 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.01 % Allowed : 29.46 % Favored : 65.53 % 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: -0.78 (0.22), residues: 1470 helix: 0.82 (0.24), residues: 560 sheet: 0.18 (0.34), residues: 234 loop : -2.00 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 60 HIS 0.002 0.001 HIS p 48 PHE 0.013 0.001 PHE f 140 TYR 0.011 0.001 TYR m 117 ARG 0.005 0.000 ARG m 56 *********************** 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 230 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 180 time to evaluate : 2.172 Fit side-chains REVERT: e 33 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6346 (tptt) REVERT: e 42 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.6171 (p-80) REVERT: e 61 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8238 (tp40) REVERT: e 204 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6730 (mt-10) REVERT: p 61 ASN cc_start: 0.7855 (p0) cc_final: 0.7629 (m110) REVERT: q 1 MET cc_start: 0.7850 (ttm) cc_final: 0.7592 (ttm) outliers start: 50 outliers final: 37 residues processed: 222 average time/residue: 1.6350 time to fit residues: 427.8061 Evaluate side-chains 219 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 166 GLN Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 113 THR Chi-restraints excluded: chain m residue 12 ARG 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 41 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 49 ASP Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain v residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 145 optimal weight: 0.0170 chunk 234 optimal weight: 2.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 40 GLN p 62 GLN q 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36076 Z= 0.149 Angle : 0.502 8.484 53953 Z= 0.261 Chirality : 0.033 0.218 6935 Planarity : 0.004 0.049 2985 Dihedral : 22.813 178.672 17932 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.11 % Allowed : 29.66 % Favored : 65.23 % 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: -0.61 (0.22), residues: 1470 helix: 0.93 (0.24), residues: 560 sheet: 0.30 (0.34), residues: 234 loop : -1.89 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 60 HIS 0.003 0.001 HIS m 96 PHE 0.013 0.001 PHE f 140 TYR 0.012 0.001 TYR m 117 ARG 0.003 0.000 ARG m 56 *********************** 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 232 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 1.964 Fit side-chains REVERT: e 33 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6324 (tptt) REVERT: e 42 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.6143 (p-80) REVERT: e 61 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8264 (tp40) REVERT: e 204 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: q 1 MET cc_start: 0.7894 (ttm) cc_final: 0.7607 (ttm) outliers start: 51 outliers final: 30 residues processed: 220 average time/residue: 1.5950 time to fit residues: 414.3761 Evaluate side-chains 214 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain m residue 12 ARG 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 41 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 49 ASP Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain v residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 40 GLN p 62 GLN q 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36076 Z= 0.256 Angle : 0.584 8.588 53953 Z= 0.300 Chirality : 0.037 0.240 6935 Planarity : 0.004 0.052 2985 Dihedral : 22.862 179.737 17931 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.91 % Allowed : 30.76 % Favored : 65.33 % 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: -0.72 (0.22), residues: 1470 helix: 0.82 (0.23), residues: 561 sheet: 0.29 (0.35), residues: 228 loop : -1.93 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 60 HIS 0.004 0.001 HIS p 48 PHE 0.014 0.001 PHE f 140 TYR 0.017 0.002 TYR m 117 ARG 0.003 0.000 ARG u 74 ********************** 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 212 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 2.341 Fit side-chains REVERT: e 33 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6398 (tptt) REVERT: e 80 GLU cc_start: 0.7738 (tp30) cc_final: 0.7532 (tm-30) REVERT: e 204 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: l 33 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7832 (mm) REVERT: q 1 MET cc_start: 0.7896 (ttm) cc_final: 0.7636 (ttm) outliers start: 39 outliers final: 33 residues processed: 206 average time/residue: 1.6997 time to fit residues: 411.4968 Evaluate side-chains 208 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 172 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 33 LYS Chi-restraints excluded: chain e residue 42 HIS Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 175 VAL Chi-restraints excluded: chain e residue 178 SER Chi-restraints excluded: chain e residue 192 ASP Chi-restraints excluded: chain e residue 204 GLU Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 33 ILE Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain m residue 12 ARG 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 41 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain q residue 73 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 71 THR Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 37 SER Chi-restraints excluded: chain u residue 74 ARG Chi-restraints excluded: chain v residue 42 THR 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: 0.0070 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 ASN i 42 GLN p 40 GLN p 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.139439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.124084 restraints weight = 37330.548| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 0.22 r_work: 0.3089 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36076 Z= 0.190 Angle : 0.559 8.329 53953 Z= 0.290 Chirality : 0.036 0.235 6935 Planarity : 0.004 0.052 2985 Dihedral : 22.861 179.356 17931 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.01 % Allowed : 30.86 % Favored : 65.13 % 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: -0.70 (0.22), residues: 1470 helix: 0.84 (0.23), residues: 561 sheet: 0.28 (0.35), residues: 228 loop : -1.92 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 60 HIS 0.003 0.001 HIS m 96 PHE 0.014 0.001 PHE f 140 TYR 0.016 0.001 TYR m 117 ARG 0.004 0.000 ARG m 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8172.08 seconds wall clock time: 147 minutes 39.38 seconds (8859.38 seconds total)