Starting phenix.real_space_refine (version: dev) on Wed Apr 6 03:27:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/04_2022/6z5u_11082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/04_2022/6z5u_11082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/04_2022/6z5u_11082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/04_2022/6z5u_11082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/04_2022/6z5u_11082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z5u_11082/04_2022/6z5u_11082_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 sd= 0.089 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E ASP 141": "OD1" <-> "OD2" Residue "K PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 17880 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1886 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'CIS': 2, 'TRANS': 244} Chain: "B" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1886 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 245} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 696 Classifications: {'peptide': 87} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 696 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 83, 'PCIS': 1} Chain: "E" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1450 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'CIS': 1, 'TRANS': 184} Chain: "G" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1461 Classifications: {'peptide': 191} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 185, 'PCIS': 1} Chain: "H" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1443 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "I" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1476 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain: "J" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1450 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'CIS': 2, 'TRANS': 183} Chain: "K" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1948 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "L" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1948 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1476 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.57, per 1000 atoms: 0.65 Number of scatterers: 17880 At special positions: 0 Unit cell: (135.89, 144.45, 145.52, 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 92 16.00 P 6 15.00 Mg 2 11.99 O 3419 8.00 N 2967 7.00 C 11394 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: 7.93 Conformation dependent library (CDL) restraints added in 2.7 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 15 sheets defined 49.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 5 through 29 Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.720A pdb=" N HIS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 78 removed outlier: 4.695A pdb=" N LEU A 54 " --> pdb=" O MET A 51 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 72 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 73 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 3.592A pdb=" N MET A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 89 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 94 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 122 removed outlier: 3.996A pdb=" N ALA A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 142 through 171 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 195 through 219 Processing helix chain 'A' and resid 225 through 254 removed outlier: 4.209A pdb=" N ILE A 228 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 229 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 239 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 252 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 254 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 30 Processing helix chain 'B' and resid 35 through 47 removed outlier: 4.048A pdb=" N GLY B 39 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL B 42 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 45 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.907A pdb=" N LEU B 54 " --> pdb=" O MET B 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 57 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 72 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 76 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 removed outlier: 5.419A pdb=" N GLY B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 removed outlier: 4.138A pdb=" N ALA B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.572A pdb=" N MET B 131 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 142 through 171 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 179 through 189 Processing helix chain 'B' and resid 192 through 218 removed outlier: 7.257A pdb=" N VAL B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 254 removed outlier: 3.506A pdb=" N ALA B 229 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 239 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 241 " --> pdb=" O TYR B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 51 through 64 removed outlier: 4.225A pdb=" N THR C 64 " --> pdb=" O TRP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.687A pdb=" N ALA D 20 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU D 21 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 24 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 65 through 68 No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'E' and resid 6 through 32 removed outlier: 5.188A pdb=" N ILE E 16 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE E 17 " --> pdb=" O PHE E 13 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 96 through 108 Processing helix chain 'E' and resid 113 through 116 No H-bonds generated for 'chain 'E' and resid 113 through 116' Processing helix chain 'E' and resid 120 through 136 removed outlier: 4.289A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'G' and resid 5 through 29 removed outlier: 5.060A pdb=" N VAL G 10 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 95 through 112 Processing helix chain 'G' and resid 115 through 118 No H-bonds generated for 'chain 'G' and resid 115 through 118' Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.684A pdb=" N ASN G 135 " --> pdb=" O ILE G 131 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 190 Processing helix chain 'H' and resid 7 through 32 removed outlier: 3.948A pdb=" N ILE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 92 through 111 removed outlier: 5.023A pdb=" N LEU H 98 " --> pdb=" O ALA H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 116 No H-bonds generated for 'chain 'H' and resid 113 through 116' Processing helix chain 'H' and resid 120 through 134 removed outlier: 4.845A pdb=" N THR H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 190 Processing helix chain 'I' and resid 3 through 30 removed outlier: 4.367A pdb=" N GLU I 7 " --> pdb=" O SER I 3 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU I 8 " --> pdb=" O ARG I 4 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY I 30 " --> pdb=" O MET I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 91 No H-bonds generated for 'chain 'I' and resid 88 through 91' Processing helix chain 'I' and resid 95 through 111 Processing helix chain 'I' and resid 115 through 117 No H-bonds generated for 'chain 'I' and resid 115 through 117' Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.877A pdb=" N MET I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN I 135 " --> pdb=" O ILE I 131 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER I 136 " --> pdb=" O SER I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 192 Processing helix chain 'J' and resid 6 through 30 removed outlier: 4.236A pdb=" N VAL J 14 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ILE J 15 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE J 16 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 111 Processing helix chain 'J' and resid 113 through 115 No H-bonds generated for 'chain 'J' and resid 113 through 115' Processing helix chain 'J' and resid 120 through 136 removed outlier: 3.550A pdb=" N THR J 125 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 192 Processing helix chain 'K' and resid 51 through 58 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 81 through 90 removed outlier: 4.053A pdb=" N ALA K 89 " --> pdb=" O PHE K 85 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 117 Proline residue: K 113 - end of helix removed outlier: 4.149A pdb=" N ALA K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS K 117 " --> pdb=" O PRO K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 136 removed outlier: 3.680A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 141 No H-bonds generated for 'chain 'K' and resid 139 through 141' Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 151 through 162 Processing helix chain 'K' and resid 175 through 177 No H-bonds generated for 'chain 'K' and resid 175 through 177' Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 209 through 211 No H-bonds generated for 'chain 'K' and resid 209 through 211' Processing helix chain 'K' and resid 233 through 238 Processing helix chain 'K' and resid 242 through 249 Processing helix chain 'L' and resid 51 through 58 Processing helix chain 'L' and resid 81 through 90 removed outlier: 4.079A pdb=" N ALA L 89 " --> pdb=" O PHE L 85 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG L 90 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 117 Proline residue: L 113 - end of helix removed outlier: 4.065A pdb=" N ALA L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS L 117 " --> pdb=" O PRO L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 136 removed outlier: 3.753A pdb=" N VAL L 136 " --> pdb=" O LYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 151 through 162 Processing helix chain 'L' and resid 181 through 197 removed outlier: 3.797A pdb=" N GLU L 196 " --> pdb=" O ARG L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 215 removed outlier: 4.141A pdb=" N SER L 214 " --> pdb=" O PRO L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 238 removed outlier: 3.717A pdb=" N ALA L 238 " --> pdb=" O GLU L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 249 Processing helix chain 'F' and resid 3 through 30 removed outlier: 4.367A pdb=" N GLU F 7 " --> pdb=" O SER F 3 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU F 8 " --> pdb=" O ARG F 4 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 91 No H-bonds generated for 'chain 'F' and resid 88 through 91' Processing helix chain 'F' and resid 95 through 111 Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 120 through 136 removed outlier: 3.877A pdb=" N MET F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN F 135 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER F 136 " --> pdb=" O SER F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 192 Processing sheet with id= A, first strand: chain 'D' and resid 40 through 42 removed outlier: 7.123A pdb=" N HIS D 71 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'E' and resid 39 through 46 removed outlier: 3.555A pdb=" N SER E 70 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP E 85 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL E 68 " --> pdb=" O ASP E 85 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP E 87 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY E 66 " --> pdb=" O ASP E 87 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET E 60 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL E 58 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 57 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 41 through 46 removed outlier: 6.350A pdb=" N ASP G 85 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL G 68 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET G 60 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL G 58 " --> pdb=" O ILE G 65 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 145 through 150 Processing sheet with id= E, first strand: chain 'H' and resid 40 through 46 removed outlier: 3.739A pdb=" N VAL H 63 " --> pdb=" O MET H 60 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET H 60 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL H 58 " --> pdb=" O ILE H 65 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 71 through 73 Processing sheet with id= G, first strand: chain 'I' and resid 40 through 46 removed outlier: 3.783A pdb=" N LEU I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL I 68 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL I 58 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU I 159 " --> pdb=" O THR I 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 40 through 46 removed outlier: 3.505A pdb=" N LEU J 79 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP J 85 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL J 68 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET J 60 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL J 58 " --> pdb=" O ILE J 65 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS J 57 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 33 through 35 Processing sheet with id= J, first strand: chain 'K' and resid 226 through 231 removed outlier: 6.456A pdb=" N VAL K 221 " --> pdb=" O GLN K 228 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU K 230 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE K 219 " --> pdb=" O GLU K 230 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR K 202 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE K 43 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE K 204 " --> pdb=" O ILE K 43 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 18 through 20 removed outlier: 7.771A pdb=" N PHE K 20 " --> pdb=" O ASP K 29 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP K 29 " --> pdb=" O PHE K 20 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 33 through 35 Processing sheet with id= M, first strand: chain 'L' and resid 226 through 231 removed outlier: 6.581A pdb=" N VAL L 221 " --> pdb=" O GLN L 228 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU L 230 " --> pdb=" O ILE L 219 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE L 219 " --> pdb=" O GLU L 230 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR L 202 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE L 43 " --> pdb=" O THR L 202 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE L 204 " --> pdb=" O ILE L 43 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 18 through 20 removed outlier: 7.745A pdb=" N PHE L 20 " --> pdb=" O ASP L 29 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASP L 29 " --> pdb=" O PHE L 20 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 40 through 46 removed outlier: 3.783A pdb=" N LEU F 79 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 70 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP F 85 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL F 68 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 58 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU F 159 " --> pdb=" O THR F 59 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 8.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3092 1.30 - 1.44: 4705 1.44 - 1.58: 10101 1.58 - 1.71: 66 1.71 - 1.85: 170 Bond restraints: 18134 Sorted by residual: bond pdb=" N3B ANP K 301 " pdb=" PG ANP K 301 " ideal model delta sigma weight residual 1.795 1.566 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" N3B ANP L 302 " pdb=" PG ANP L 302 " ideal model delta sigma weight residual 1.795 1.568 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" O3A ANP L 302 " pdb=" PB ANP L 302 " ideal model delta sigma weight residual 1.700 1.487 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" O3A ANP K 301 " pdb=" PB ANP K 301 " ideal model delta sigma weight residual 1.700 1.517 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" CB HIS L 207 " pdb=" CG HIS L 207 " ideal model delta sigma weight residual 1.497 1.379 0.118 1.40e-02 5.10e+03 7.06e+01 ... (remaining 18129 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.95: 261 103.95 - 112.31: 8606 112.31 - 120.68: 10215 120.68 - 129.04: 5405 129.04 - 137.40: 57 Bond angle restraints: 24544 Sorted by residual: angle pdb=" N SER K 206 " pdb=" CA SER K 206 " pdb=" C SER K 206 " ideal model delta sigma weight residual 108.19 122.23 -14.04 1.29e+00 6.01e-01 1.18e+02 angle pdb=" C ASP H 74 " pdb=" N PRO H 75 " pdb=" CA PRO H 75 " ideal model delta sigma weight residual 119.56 128.59 -9.03 1.02e+00 9.61e-01 7.84e+01 angle pdb=" N THR G 77 " pdb=" CA THR G 77 " pdb=" C THR G 77 " ideal model delta sigma weight residual 114.31 103.34 10.97 1.29e+00 6.01e-01 7.23e+01 angle pdb=" N ILE L 27 " pdb=" CA ILE L 27 " pdb=" C ILE L 27 " ideal model delta sigma weight residual 111.81 104.76 7.05 8.60e-01 1.35e+00 6.72e+01 angle pdb=" CA PHE H 22 " pdb=" CB PHE H 22 " pdb=" CG PHE H 22 " ideal model delta sigma weight residual 113.80 105.64 8.16 1.00e+00 1.00e+00 6.67e+01 ... (remaining 24539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 10357 18.13 - 36.27: 368 36.27 - 54.40: 120 54.40 - 72.53: 40 72.53 - 90.67: 11 Dihedral angle restraints: 10896 sinusoidal: 4266 harmonic: 6630 Sorted by residual: dihedral pdb=" CA MET L 79 " pdb=" C MET L 79 " pdb=" N SER L 80 " pdb=" CA SER L 80 " ideal model delta harmonic sigma weight residual -180.00 -89.33 -90.67 0 5.00e+00 4.00e-02 3.29e+02 dihedral pdb=" C GLU K 211 " pdb=" N GLU K 211 " pdb=" CA GLU K 211 " pdb=" CB GLU K 211 " ideal model delta harmonic sigma weight residual -122.60 -141.52 18.92 0 2.50e+00 1.60e-01 5.73e+01 dihedral pdb=" N GLU K 211 " pdb=" C GLU K 211 " pdb=" CA GLU K 211 " pdb=" CB GLU K 211 " ideal model delta harmonic sigma weight residual 122.80 140.13 -17.33 0 2.50e+00 1.60e-01 4.81e+01 ... (remaining 10893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2505 0.148 - 0.297: 412 0.297 - 0.445: 22 0.445 - 0.593: 7 0.593 - 0.742: 1 Chirality restraints: 2947 Sorted by residual: chirality pdb=" CA GLU K 211 " pdb=" N GLU K 211 " pdb=" C GLU K 211 " pdb=" CB GLU K 211 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA VAL K 209 " pdb=" N VAL K 209 " pdb=" C VAL K 209 " pdb=" CB VAL K 209 " both_signs ideal model delta sigma weight residual False 2.44 1.86 0.58 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA LEU G 36 " pdb=" N LEU G 36 " pdb=" C LEU G 36 " pdb=" CB LEU G 36 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 2944 not shown) Planarity restraints: 3103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP L 302 " -0.629 2.00e-02 2.50e+03 2.45e-01 1.65e+03 pdb=" C2 ANP L 302 " 0.071 2.00e-02 2.50e+03 pdb=" C4 ANP L 302 " 0.180 2.00e-02 2.50e+03 pdb=" C5 ANP L 302 " 0.029 2.00e-02 2.50e+03 pdb=" C6 ANP L 302 " -0.095 2.00e-02 2.50e+03 pdb=" C8 ANP L 302 " 0.221 2.00e-02 2.50e+03 pdb=" N1 ANP L 302 " -0.074 2.00e-02 2.50e+03 pdb=" N3 ANP L 302 " 0.206 2.00e-02 2.50e+03 pdb=" N6 ANP L 302 " -0.228 2.00e-02 2.50e+03 pdb=" N7 ANP L 302 " 0.063 2.00e-02 2.50e+03 pdb=" N9 ANP L 302 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP K 301 " -0.550 2.00e-02 2.50e+03 2.15e-01 1.27e+03 pdb=" C2 ANP K 301 " 0.058 2.00e-02 2.50e+03 pdb=" C4 ANP K 301 " 0.157 2.00e-02 2.50e+03 pdb=" C5 ANP K 301 " 0.034 2.00e-02 2.50e+03 pdb=" C6 ANP K 301 " -0.080 2.00e-02 2.50e+03 pdb=" C8 ANP K 301 " 0.191 2.00e-02 2.50e+03 pdb=" N1 ANP K 301 " -0.068 2.00e-02 2.50e+03 pdb=" N3 ANP K 301 " 0.174 2.00e-02 2.50e+03 pdb=" N6 ANP K 301 " -0.208 2.00e-02 2.50e+03 pdb=" N7 ANP K 301 " 0.061 2.00e-02 2.50e+03 pdb=" N9 ANP K 301 " 0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 158 " 0.226 2.00e-02 2.50e+03 1.16e-01 2.70e+02 pdb=" CG TYR H 158 " -0.113 2.00e-02 2.50e+03 pdb=" CD1 TYR H 158 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR H 158 " -0.098 2.00e-02 2.50e+03 pdb=" CE1 TYR H 158 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR H 158 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR H 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 158 " 0.153 2.00e-02 2.50e+03 ... (remaining 3100 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.70: 20 1.70 - 2.50: 59 2.50 - 3.30: 22096 3.30 - 4.10: 42617 4.10 - 4.90: 74922 Warning: very small nonbonded interaction distances. Nonbonded interactions: 139714 Sorted by model distance: nonbonded pdb=" OG1 THR G 194 " pdb=" CD1 PHE F 192 " model vdw 0.901 3.340 nonbonded pdb=" CB THR G 194 " pdb=" CZ PHE F 192 " model vdw 0.902 3.770 nonbonded pdb=" CB THR G 194 " pdb=" CE1 PHE F 192 " model vdw 0.915 3.770 nonbonded pdb=" O THR G 194 " pdb=" CE LYS F 191 " model vdw 1.062 3.440 nonbonded pdb=" CE MET E 183 " pdb=" CD GLU F 186 " model vdw 1.065 3.690 ... (remaining 139709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 6 through 194) selection = (chain 'F' and resid 6 through 194) selection = (chain 'G' and resid 6 through 194) selection = chain 'H' selection = (chain 'I' and resid 6 through 194) selection = (chain 'J' and resid 6 through 194) } ncs_group { reference = (chain 'K' and resid 11 through 263) selection = (chain 'L' and resid 11 through 263) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 11394 2.51 5 N 2967 2.21 5 O 3419 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.020 Extract box with map and model: 5.210 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.140 Process input model: 49.480 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0317 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 : 0.021 0.229 18134 Z= 1.357 Angle : 1.880 15.582 24544 Z= 1.253 Chirality : 0.107 0.742 2947 Planarity : 0.012 0.245 3103 Dihedral : 11.925 90.668 6648 Min Nonbonded Distance : 0.901 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.03 % Favored : 97.66 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.47 (0.16), residues: 2310 helix: -0.27 (0.14), residues: 1070 sheet: 0.88 (0.33), residues: 259 loop : -0.53 (0.18), residues: 981 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 8 residues processed: 280 average time/residue: 0.2955 time to fit residues: 124.5756 Evaluate side-chains 176 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1542 time to fit residues: 5.1967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 92 optimal weight: 0.0770 chunk 179 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN B 77 ASN B 189 ASN C 74 ASN D 84 GLN K 207 HIS L 96 GLN L 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0793 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 18134 Z= 0.286 Angle : 0.820 12.270 24544 Z= 0.431 Chirality : 0.048 0.315 2947 Planarity : 0.006 0.046 3103 Dihedral : 6.180 59.514 2475 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.40 (0.16), residues: 2310 helix: 0.20 (0.15), residues: 1069 sheet: 0.27 (0.30), residues: 259 loop : -0.83 (0.19), residues: 982 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 208 average time/residue: 0.2847 time to fit residues: 91.5466 Evaluate side-chains 170 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2033 time to fit residues: 7.6741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 0.0570 chunk 64 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 225 optimal weight: 0.6980 chunk 185 optimal weight: 8.9990 chunk 206 optimal weight: 0.0270 chunk 71 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0927 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 18134 Z= 0.193 Angle : 0.687 12.582 24544 Z= 0.358 Chirality : 0.043 0.211 2947 Planarity : 0.005 0.051 3103 Dihedral : 5.386 50.795 2475 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.35 (0.17), residues: 2310 helix: 0.35 (0.15), residues: 1087 sheet: 0.12 (0.29), residues: 267 loop : -0.91 (0.19), residues: 956 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 188 average time/residue: 0.2696 time to fit residues: 79.8742 Evaluate side-chains 176 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1674 time to fit residues: 7.3246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 209 optimal weight: 20.0000 chunk 221 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 59 optimal weight: 30.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1079 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 18134 Z= 0.175 Angle : 0.639 11.175 24544 Z= 0.327 Chirality : 0.042 0.162 2947 Planarity : 0.005 0.041 3103 Dihedral : 5.131 42.148 2475 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.35 (0.17), residues: 2310 helix: 0.40 (0.16), residues: 1083 sheet: -0.06 (0.29), residues: 267 loop : -0.92 (0.19), residues: 960 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 166 average time/residue: 0.2691 time to fit residues: 70.5349 Evaluate side-chains 161 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1590 time to fit residues: 6.3584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 153 optimal weight: 0.0070 chunk 0 optimal weight: 9.9990 chunk 113 optimal weight: 0.3980 chunk 198 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN K 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1115 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.120 18134 Z= 0.171 Angle : 0.627 15.466 24544 Z= 0.324 Chirality : 0.042 0.204 2947 Planarity : 0.004 0.048 3103 Dihedral : 4.968 39.869 2475 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.29 (0.17), residues: 2310 helix: 0.46 (0.16), residues: 1095 sheet: -0.06 (0.30), residues: 264 loop : -0.90 (0.19), residues: 951 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 168 average time/residue: 0.2754 time to fit residues: 73.8188 Evaluate side-chains 160 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2159 time to fit residues: 7.2079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 43 optimal weight: 0.0030 chunk 129 optimal weight: 0.0870 chunk 54 optimal weight: 8.9990 chunk 221 optimal weight: 30.0000 chunk 183 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN H 94 ASN L 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1098 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.179 18134 Z= 0.155 Angle : 0.617 19.068 24544 Z= 0.320 Chirality : 0.041 0.185 2947 Planarity : 0.004 0.082 3103 Dihedral : 4.768 36.559 2475 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % 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: -0.11 (0.17), residues: 2310 helix: 0.67 (0.16), residues: 1077 sheet: 0.00 (0.30), residues: 268 loop : -0.88 (0.19), residues: 965 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 160 average time/residue: 0.2691 time to fit residues: 69.1144 Evaluate side-chains 155 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1642 time to fit residues: 5.2440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 161 optimal weight: 0.1980 chunk 125 optimal weight: 0.0370 chunk 186 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 220 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 101 optimal weight: 0.1980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1123 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.224 18134 Z= 0.182 Angle : 0.624 23.075 24544 Z= 0.322 Chirality : 0.041 0.183 2947 Planarity : 0.004 0.058 3103 Dihedral : 4.590 33.795 2475 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.23 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % 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: -0.04 (0.17), residues: 2310 helix: 0.81 (0.16), residues: 1077 sheet: -0.05 (0.30), residues: 274 loop : -0.93 (0.19), residues: 959 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 160 average time/residue: 0.3000 time to fit residues: 76.3646 Evaluate side-chains 154 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.986 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1719 time to fit residues: 4.3283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 0.0020 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN G 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1176 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.069 18134 Z= 0.144 Angle : 0.596 16.556 24544 Z= 0.303 Chirality : 0.041 0.232 2947 Planarity : 0.004 0.047 3103 Dihedral : 4.515 32.247 2475 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.97 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % 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: 0.01 (0.17), residues: 2310 helix: 0.88 (0.16), residues: 1078 sheet: -0.07 (0.30), residues: 274 loop : -0.91 (0.20), residues: 958 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 155 average time/residue: 0.2660 time to fit residues: 65.8426 Evaluate side-chains 154 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1694 time to fit residues: 4.0652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 10.0000 chunk 211 optimal weight: 0.8980 chunk 192 optimal weight: 0.1980 chunk 205 optimal weight: 4.9990 chunk 123 optimal weight: 0.0870 chunk 89 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 198 ASN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1197 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.080 18134 Z= 0.618 Angle : 0.889 93.689 24544 Z= 0.395 Chirality : 0.041 0.275 2947 Planarity : 0.004 0.062 3103 Dihedral : 4.482 31.018 2475 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % 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: -0.03 (0.17), residues: 2310 helix: 0.83 (0.16), residues: 1080 sheet: -0.09 (0.30), residues: 274 loop : -0.93 (0.20), residues: 956 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 156 average time/residue: 0.2779 time to fit residues: 68.5998 Evaluate side-chains 149 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1597 time to fit residues: 4.0353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 6.9990 chunk 217 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 151 optimal weight: 50.0000 chunk 228 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 140 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1232 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.272 18134 Z= 0.164 Angle : 0.624 27.209 24544 Z= 0.333 Chirality : 0.041 0.214 2947 Planarity : 0.005 0.163 3103 Dihedral : 4.429 29.758 2475 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.84 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % 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: 0.01 (0.17), residues: 2310 helix: 0.89 (0.16), residues: 1079 sheet: -0.13 (0.30), residues: 274 loop : -0.91 (0.20), residues: 957 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.2974 time to fit residues: 69.5058 Evaluate side-chains 142 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1554 time to fit residues: 3.1763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 0.0270 chunk 193 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 50.0000 chunk 181 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5596 r_free = 0.5596 target = 0.349434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5437 r_free = 0.5437 target = 0.325098 restraints weight = 33778.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5483 r_free = 0.5483 target = 0.331933 restraints weight = 19756.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.5513 r_free = 0.5513 target = 0.336659 restraints weight = 12399.946| |-----------------------------------------------------------------------------| r_work (final): 0.5477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1320 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.778 18134 Z= 0.499 Angle : 0.802 62.353 24544 Z= 0.458 Chirality : 0.042 0.221 2947 Planarity : 0.005 0.153 3103 Dihedral : 4.452 30.382 2475 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.35 % 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: -0.06 (0.18), residues: 2310 helix: 0.85 (0.16), residues: 1077 sheet: -0.22 (0.30), residues: 286 loop : -0.95 (0.20), residues: 947 =============================================================================== Job complete usr+sys time: 2936.15 seconds wall clock time: 54 minutes 50.47 seconds (3290.47 seconds total)