Starting phenix.real_space_refine (version: dev) on Mon Apr 4 20:06:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2022/7m05_23609_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2022/7m05_23609.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2022/7m05_23609_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2022/7m05_23609_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2022/7m05_23609_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2022/7m05_23609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2022/7m05_23609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2022/7m05_23609_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m05_23609/04_2022/7m05_23609_trim_updated.pdb" } resolution = 2.39 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= 0.000 sd= 1.000 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 "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 57152 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9868 Classifications: {'peptide': 615} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 570, 'PCIS': 5} Chain breaks: 2 Chain: "B" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4389 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 281, 'PCIS': 1} Chain breaks: 2 Chain: "C" Number of atoms: 9868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9868 Classifications: {'peptide': 615} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 570, 'PCIS': 5} Chain breaks: 2 Chain: "D" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4389 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 281, 'PCIS': 1} Chain breaks: 2 Chain: "E" Number of atoms: 9868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9868 Classifications: {'peptide': 615} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 570, 'PCIS': 5} Chain breaks: 2 Chain: "F" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4389 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 281, 'PCIS': 1} Chain breaks: 2 Chain: "G" Number of atoms: 9868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9868 Classifications: {'peptide': 615} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 570, 'PCIS': 5} Chain breaks: 2 Chain: "H" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4389 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 281, 'PCIS': 1} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'YJG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'YJG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'YJG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'YJG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.96, per 1000 atoms: 0.33 Number of scatterers: 57152 At special positions: 0 Unit cell: (126.36, 143.64, 137.16, 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) Cl 4 17.00 S 148 16.00 O 5400 8.00 N 4960 7.00 C 18452 6.00 H 28188 1.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 34.08 Conformation dependent library (CDL) restraints added in 3.5 seconds 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 52 sheets defined 20.4% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 97 through 117 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.571A pdb=" N TRP A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.678A pdb=" N LYS A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.674A pdb=" N LYS A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 395 through 407 removed outlier: 3.749A pdb=" N THR A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 478 through 487 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 75 through 81 Processing helix chain 'C' and resid 97 through 117 Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.571A pdb=" N TRP C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 248 through 260 removed outlier: 3.679A pdb=" N LYS C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 289 Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'C' and resid 321 through 329 removed outlier: 3.674A pdb=" N LYS C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 348 Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 395 through 407 removed outlier: 3.749A pdb=" N THR C 400 " --> pdb=" O ASN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 451 Processing helix chain 'C' and resid 478 through 487 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 75 through 81 Processing helix chain 'E' and resid 97 through 117 Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 184 through 196 removed outlier: 3.571A pdb=" N TRP E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.678A pdb=" N LYS E 259 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 289 Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 321 through 329 removed outlier: 3.674A pdb=" N LYS E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 348 Processing helix chain 'E' and resid 370 through 382 Processing helix chain 'E' and resid 395 through 407 removed outlier: 3.748A pdb=" N THR E 400 " --> pdb=" O ASN E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 451 Processing helix chain 'E' and resid 478 through 487 Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 628 through 630 No H-bonds generated for 'chain 'E' and resid 628 through 630' Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 75 through 81 Processing helix chain 'G' and resid 97 through 117 Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 184 through 196 removed outlier: 3.571A pdb=" N TRP G 189 " --> pdb=" O THR G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 220 Processing helix chain 'G' and resid 233 through 235 No H-bonds generated for 'chain 'G' and resid 233 through 235' Processing helix chain 'G' and resid 248 through 260 removed outlier: 3.679A pdb=" N LYS G 259 " --> pdb=" O PHE G 255 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 289 Processing helix chain 'G' and resid 296 through 300 Processing helix chain 'G' and resid 321 through 329 removed outlier: 3.674A pdb=" N LYS G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 348 Processing helix chain 'G' and resid 370 through 382 Processing helix chain 'G' and resid 395 through 407 removed outlier: 3.749A pdb=" N THR G 400 " --> pdb=" O ASN G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 451 Processing helix chain 'G' and resid 478 through 487 Processing helix chain 'G' and resid 496 through 498 No H-bonds generated for 'chain 'G' and resid 496 through 498' Processing helix chain 'G' and resid 628 through 630 No H-bonds generated for 'chain 'G' and resid 628 through 630' Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing sheet with id= A, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.600A pdb=" N PHE A 40 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 264 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP A 19 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 266 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS A 227 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL A 204 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA A 229 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU A 231 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 151 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA A 205 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET A 153 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU A 207 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 155 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 462 through 464 Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.554A pdb=" N GLU A 467 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 550 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 582 " --> pdb=" O GLY A 553 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 534 through 541 Processing sheet with id= E, first strand: chain 'A' and resid 546 through 548 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.890A pdb=" N ILE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 75 through 79 removed outlier: 3.735A pdb=" N GLY B 56 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 33 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER B 47 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU B 31 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.600A pdb=" N ALA B 97 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B 86 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 95 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP B 88 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY B 93 " --> pdb=" O TRP B 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 98 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU B 107 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER B 117 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 128 through 133 removed outlier: 6.990A pdb=" N GLY B 143 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL B 131 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 141 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL B 133 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN B 139 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 161 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 153 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL B 159 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 203 through 205 removed outlier: 3.673A pdb=" N PHE B 183 " --> pdb=" O TRP B 195 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS B 172 " --> pdb=" O CYS B 186 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 249 through 252 removed outlier: 4.430A pdb=" N THR B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 217 " --> pdb=" O GLY B 231 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 258 through 263 removed outlier: 6.930A pdb=" N LEU B 274 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU B 261 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 272 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 291 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 323 through 326 removed outlier: 3.988A pdb=" N ASP B 302 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 40 through 42 removed outlier: 3.600A pdb=" N PHE C 40 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE C 264 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP C 19 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 266 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS C 227 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL C 204 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA C 229 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 206 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU C 231 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE C 151 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 205 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET C 153 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU C 207 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 155 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 462 through 464 Processing sheet with id= P, first strand: chain 'C' and resid 520 through 522 removed outlier: 3.554A pdb=" N GLU C 467 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 550 " --> pdb=" O ILE C 475 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 582 " --> pdb=" O GLY C 553 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 534 through 541 Processing sheet with id= R, first strand: chain 'C' and resid 546 through 548 Processing sheet with id= S, first strand: chain 'C' and resid 556 through 560 removed outlier: 6.890A pdb=" N ILE C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 75 through 79 removed outlier: 3.736A pdb=" N GLY D 56 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 33 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER D 47 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU D 31 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.600A pdb=" N ALA D 97 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 86 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU D 95 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP D 88 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY D 93 " --> pdb=" O TRP D 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 98 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU D 107 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER D 117 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 128 through 133 removed outlier: 6.991A pdb=" N GLY D 143 " --> pdb=" O SER D 129 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL D 131 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL D 141 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL D 133 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN D 139 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 161 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP D 153 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL D 159 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 203 through 205 removed outlier: 3.673A pdb=" N PHE D 183 " --> pdb=" O TRP D 195 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS D 172 " --> pdb=" O CYS D 186 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 249 through 252 removed outlier: 4.430A pdb=" N THR D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER D 217 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 258 through 263 removed outlier: 6.929A pdb=" N LEU D 274 " --> pdb=" O THR D 259 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU D 261 " --> pdb=" O ALA D 272 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA D 272 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 291 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 323 through 326 removed outlier: 3.987A pdb=" N ASP D 302 " --> pdb=" O VAL D 316 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 82 through 85 removed outlier: 6.562A pdb=" N LEU E 41 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LYS E 85 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET E 43 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE E 40 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE E 264 " --> pdb=" O GLY E 17 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP E 19 " --> pdb=" O PHE E 264 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE E 266 " --> pdb=" O ASP E 19 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS E 227 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 204 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA E 229 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU E 206 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU E 231 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE E 151 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA E 205 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET E 153 " --> pdb=" O ALA E 205 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU E 207 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 155 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 462 through 464 Processing sheet with id= AC, first strand: chain 'E' and resid 520 through 522 removed outlier: 3.555A pdb=" N GLU E 467 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 550 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 582 " --> pdb=" O GLY E 553 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 534 through 541 Processing sheet with id= AE, first strand: chain 'E' and resid 546 through 548 Processing sheet with id= AF, first strand: chain 'E' and resid 556 through 560 removed outlier: 6.890A pdb=" N ILE E 563 " --> pdb=" O LEU E 559 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 75 through 79 removed outlier: 3.735A pdb=" N GLY F 56 " --> pdb=" O THR F 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 33 " --> pdb=" O GLY F 45 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER F 47 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU F 31 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 83 through 89 removed outlier: 6.599A pdb=" N ALA F 97 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU F 86 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU F 95 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP F 88 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY F 93 " --> pdb=" O TRP F 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 98 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU F 107 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER F 117 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 128 through 133 removed outlier: 6.990A pdb=" N GLY F 143 " --> pdb=" O SER F 129 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL F 131 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL F 141 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL F 133 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN F 139 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 161 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP F 153 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL F 159 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 203 through 205 removed outlier: 3.673A pdb=" N PHE F 183 " --> pdb=" O TRP F 195 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS F 172 " --> pdb=" O CYS F 186 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 249 through 252 removed outlier: 4.430A pdb=" N THR F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER F 217 " --> pdb=" O GLY F 231 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 258 through 263 removed outlier: 6.929A pdb=" N LEU F 274 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU F 261 " --> pdb=" O ALA F 272 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA F 272 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE F 291 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 323 through 326 removed outlier: 3.988A pdb=" N ASP F 302 " --> pdb=" O VAL F 316 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 40 through 42 removed outlier: 3.600A pdb=" N PHE G 40 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE G 264 " --> pdb=" O GLY G 17 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP G 19 " --> pdb=" O PHE G 264 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE G 266 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS G 227 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL G 204 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA G 229 " --> pdb=" O VAL G 204 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU G 206 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU G 231 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE G 151 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA G 205 " --> pdb=" O PHE G 151 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET G 153 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU G 207 " --> pdb=" O MET G 153 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL G 155 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 462 through 464 Processing sheet with id= AP, first strand: chain 'G' and resid 520 through 522 removed outlier: 3.554A pdb=" N GLU G 467 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY G 550 " --> pdb=" O ILE G 475 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 582 " --> pdb=" O GLY G 553 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 534 through 541 Processing sheet with id= AR, first strand: chain 'G' and resid 546 through 548 Processing sheet with id= AS, first strand: chain 'G' and resid 556 through 560 removed outlier: 6.890A pdb=" N ILE G 563 " --> pdb=" O LEU G 559 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 75 through 79 removed outlier: 3.736A pdb=" N GLY H 56 " --> pdb=" O THR H 79 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 33 " --> pdb=" O GLY H 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER H 47 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LEU H 31 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'H' and resid 83 through 89 removed outlier: 6.600A pdb=" N ALA H 97 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU H 86 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU H 95 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP H 88 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY H 93 " --> pdb=" O TRP H 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER H 98 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA H 102 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU H 107 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER H 117 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 128 through 133 removed outlier: 6.991A pdb=" N GLY H 143 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL H 131 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL H 141 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL H 133 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN H 139 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER H 161 " --> pdb=" O VAL H 151 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP H 153 " --> pdb=" O VAL H 159 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL H 159 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 203 through 205 removed outlier: 3.672A pdb=" N PHE H 183 " --> pdb=" O TRP H 195 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS H 172 " --> pdb=" O CYS H 186 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 249 through 252 removed outlier: 4.430A pdb=" N THR H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER H 217 " --> pdb=" O GLY H 231 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'H' and resid 258 through 263 removed outlier: 6.930A pdb=" N LEU H 274 " --> pdb=" O THR H 259 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU H 261 " --> pdb=" O ALA H 272 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA H 272 " --> pdb=" O LEU H 261 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 291 " --> pdb=" O VAL H 282 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 323 through 326 removed outlier: 3.988A pdb=" N ASP H 302 " --> pdb=" O VAL H 316 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2604 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: 19.09 Time building geometry restraints manager: 36.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 28100 1.02 - 1.22: 88 1.22 - 1.42: 12700 1.42 - 1.62: 16816 1.62 - 1.82: 208 Bond restraints: 57912 Sorted by residual: bond pdb=" C12 YJG A 701 " pdb=" N11 YJG A 701 " ideal model delta sigma weight residual 1.478 1.285 0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" C12 YJG E 701 " pdb=" N11 YJG E 701 " ideal model delta sigma weight residual 1.478 1.285 0.193 2.00e-02 2.50e+03 9.30e+01 bond pdb=" C12 YJG C 701 " pdb=" N11 YJG C 701 " ideal model delta sigma weight residual 1.478 1.286 0.192 2.00e-02 2.50e+03 9.25e+01 bond pdb=" C12 YJG G 701 " pdb=" N11 YJG G 701 " ideal model delta sigma weight residual 1.478 1.286 0.192 2.00e-02 2.50e+03 9.25e+01 bond pdb=" C13 YJG A 701 " pdb=" C14 YJG A 701 " ideal model delta sigma weight residual 1.464 1.329 0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 57907 not shown) Histogram of bond angle deviations from ideal: 70.85 - 84.95: 5 84.95 - 99.06: 26 99.06 - 113.17: 68180 113.17 - 127.27: 35860 127.27 - 141.38: 473 Bond angle restraints: 104544 Sorted by residual: angle pdb=" C04 YJG E 701 " pdb=" C05 YJG E 701 " pdb=" N06 YJG E 701 " ideal model delta sigma weight residual 86.06 124.48 -38.42 3.00e+00 1.11e-01 1.64e+02 angle pdb=" C04 YJG G 701 " pdb=" C05 YJG G 701 " pdb=" N06 YJG G 701 " ideal model delta sigma weight residual 86.06 124.40 -38.34 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C04 YJG C 701 " pdb=" C05 YJG C 701 " pdb=" N06 YJG C 701 " ideal model delta sigma weight residual 86.06 124.40 -38.34 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C04 YJG A 701 " pdb=" C05 YJG A 701 " pdb=" N06 YJG A 701 " ideal model delta sigma weight residual 86.06 124.38 -38.32 3.00e+00 1.11e-01 1.63e+02 angle pdb=" CG2 THR E 238 " pdb=" CB THR E 238 " pdb=" HB THR E 238 " ideal model delta sigma weight residual 108.00 70.85 37.15 3.00e+00 1.11e-01 1.53e+02 ... (remaining 104539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 21812 22.40 - 44.80: 1295 44.80 - 67.20: 241 67.20 - 89.60: 44 89.60 - 111.99: 4 Dihedral angle restraints: 23396 sinusoidal: 10688 harmonic: 12708 Sorted by residual: dihedral pdb=" CA SER C 606 " pdb=" C SER C 606 " pdb=" N ASN C 607 " pdb=" CA ASN C 607 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA SER G 606 " pdb=" C SER G 606 " pdb=" N ASN G 607 " pdb=" CA ASN G 607 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA SER A 606 " pdb=" C SER A 606 " pdb=" N ASN A 607 " pdb=" CA ASN A 607 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 23393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2413 0.043 - 0.086: 1369 0.086 - 0.129: 591 0.129 - 0.172: 71 0.172 - 0.215: 4 Chirality restraints: 4448 Sorted by residual: chirality pdb=" CB THR C 238 " pdb=" CA THR C 238 " pdb=" OG1 THR C 238 " pdb=" CG2 THR C 238 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR G 238 " pdb=" CA THR G 238 " pdb=" OG1 THR G 238 " pdb=" CG2 THR G 238 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 4445 not shown) Planarity restraints: 8620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 21 " -0.021 2.00e-02 2.50e+03 2.36e-02 8.39e+00 pdb=" CG ASN A 21 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 21 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 21 " -0.010 2.00e-02 2.50e+03 pdb="HD21 ASN A 21 " 0.039 2.00e-02 2.50e+03 pdb="HD22 ASN A 21 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 21 " -0.021 2.00e-02 2.50e+03 2.36e-02 8.39e+00 pdb=" CG ASN G 21 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN G 21 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN G 21 " -0.010 2.00e-02 2.50e+03 pdb="HD21 ASN G 21 " 0.039 2.00e-02 2.50e+03 pdb="HD22 ASN G 21 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 21 " 0.021 2.00e-02 2.50e+03 2.36e-02 8.39e+00 pdb=" CG ASN C 21 " 0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN C 21 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 21 " 0.011 2.00e-02 2.50e+03 pdb="HD21 ASN C 21 " -0.039 2.00e-02 2.50e+03 pdb="HD22 ASN C 21 " 0.029 2.00e-02 2.50e+03 ... (remaining 8617 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 1777 2.12 - 2.74: 102459 2.74 - 3.36: 150205 3.36 - 3.98: 209831 3.98 - 4.60: 327095 Nonbonded interactions: 791367 Sorted by model distance: nonbonded pdb=" HB THR E 238 " pdb=" HG1 THR E 238 " model vdw 1.506 1.816 nonbonded pdb=" O ALA A 135 " pdb=" HG1 THR A 139 " model vdw 1.515 1.850 nonbonded pdb=" O ALA C 135 " pdb=" HG1 THR C 139 " model vdw 1.515 1.850 nonbonded pdb=" O ALA G 135 " pdb=" HG1 THR G 139 " model vdw 1.515 1.850 nonbonded pdb=" O ALA E 135 " pdb=" HG1 THR E 139 " model vdw 1.522 1.850 ... (remaining 791362 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 S 148 5.16 5 Cl 4 4.86 5 C 18452 2.51 5 N 4960 2.21 5 O 5400 1.98 5 H 28188 0.53 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.600 Extract box with map and model: 10.380 Check model and map are aligned: 0.610 Convert atoms to be neutral: 0.360 Process input model: 128.100 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.013 0.193 29724 Z= 0.882 Angle : 1.005 38.416 40476 Z= 0.487 Chirality : 0.058 0.215 4448 Planarity : 0.007 0.060 5232 Dihedral : 14.777 111.995 10784 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.91 % Favored : 92.31 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.12), residues: 3588 helix: -1.82 (0.15), residues: 808 sheet: -1.17 (0.14), residues: 1124 loop : -2.66 (0.13), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 591 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 603 average time/residue: 2.8210 time to fit residues: 1949.4387 Evaluate side-chains 298 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 291 time to evaluate : 3.422 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 4.2705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 184 optimal weight: 0.4980 chunk 145 optimal weight: 0.7980 chunk 282 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 326 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 290 ASN B 221 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 290 ASN D 178 HIS D 221 HIS ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN E 140 ASN F 178 HIS F 221 HIS G 36 GLN G 290 ASN H 178 HIS H 221 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 29724 Z= 0.161 Angle : 0.592 15.459 40476 Z= 0.298 Chirality : 0.048 1.272 4448 Planarity : 0.004 0.047 5232 Dihedral : 6.866 83.280 3932 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.56 % Favored : 97.32 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -1.44 (0.13), residues: 3588 helix: 0.37 (0.18), residues: 808 sheet: -0.63 (0.14), residues: 1144 loop : -1.85 (0.14), residues: 1636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 326 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 349 average time/residue: 2.2226 time to fit residues: 931.6123 Evaluate side-chains 292 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 280 time to evaluate : 3.429 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 5 average time/residue: 1.4676 time to fit residues: 13.8909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 324 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 190 ASN C 61 ASN G 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 29724 Z= 0.265 Angle : 0.625 13.387 40476 Z= 0.322 Chirality : 0.050 1.389 4448 Planarity : 0.005 0.055 5232 Dihedral : 7.111 90.387 3932 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.87 (0.13), residues: 3588 helix: 0.98 (0.18), residues: 812 sheet: -0.41 (0.14), residues: 1132 loop : -1.47 (0.14), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 297 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 25 residues processed: 341 average time/residue: 2.2900 time to fit residues: 924.9347 Evaluate side-chains 300 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 275 time to evaluate : 3.430 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 1.4448 time to fit residues: 13.6064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 347 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 311 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8084 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 29724 Z= 0.311 Angle : 0.627 11.541 40476 Z= 0.330 Chirality : 0.051 1.429 4448 Planarity : 0.005 0.062 5232 Dihedral : 7.015 88.090 3932 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3588 helix: 1.08 (0.18), residues: 816 sheet: -0.34 (0.14), residues: 1132 loop : -1.23 (0.15), residues: 1640 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 274 time to evaluate : 3.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 29 residues processed: 315 average time/residue: 2.2250 time to fit residues: 835.9040 Evaluate side-chains 295 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 266 time to evaluate : 3.499 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 1.8263 time to fit residues: 22.2590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 296 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 29724 Z= 0.202 Angle : 0.553 11.400 40476 Z= 0.287 Chirality : 0.049 1.421 4448 Planarity : 0.004 0.039 5232 Dihedral : 6.722 84.625 3932 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.35 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.32 (0.14), residues: 3588 helix: 1.56 (0.19), residues: 816 sheet: -0.28 (0.14), residues: 1156 loop : -1.03 (0.15), residues: 1616 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 282 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 31 residues processed: 317 average time/residue: 2.1698 time to fit residues: 821.4014 Evaluate side-chains 281 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 250 time to evaluate : 3.483 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 29 residues processed: 2 average time/residue: 1.9019 time to fit residues: 8.9660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.7980 chunk 313 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 348 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 29724 Z= 0.189 Angle : 0.550 11.451 40476 Z= 0.284 Chirality : 0.049 1.423 4448 Planarity : 0.004 0.039 5232 Dihedral : 6.536 81.328 3932 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.01 % Favored : 96.88 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.05 (0.14), residues: 3588 helix: 1.98 (0.19), residues: 792 sheet: -0.13 (0.15), residues: 1132 loop : -0.77 (0.15), residues: 1664 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 263 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 37 residues processed: 308 average time/residue: 2.1380 time to fit residues: 798.7640 Evaluate side-chains 291 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 3.468 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 5 average time/residue: 1.9781 time to fit residues: 16.4381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 346 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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: 0.8064 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 29724 Z= 0.214 Angle : 0.557 11.469 40476 Z= 0.289 Chirality : 0.049 1.427 4448 Planarity : 0.004 0.042 5232 Dihedral : 6.552 82.686 3932 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.01 (0.14), residues: 3588 helix: 1.77 (0.19), residues: 816 sheet: -0.12 (0.15), residues: 1140 loop : -0.80 (0.15), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 264 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 36 residues processed: 303 average time/residue: 2.1542 time to fit residues: 790.8992 Evaluate side-chains 288 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 3.458 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 5 average time/residue: 1.8335 time to fit residues: 15.6812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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: 0.8062 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 29724 Z= 0.206 Angle : 0.554 11.468 40476 Z= 0.288 Chirality : 0.049 1.425 4448 Planarity : 0.004 0.041 5232 Dihedral : 6.480 82.596 3932 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.08 (0.14), residues: 3588 helix: 1.90 (0.19), residues: 792 sheet: -0.07 (0.15), residues: 1140 loop : -0.72 (0.15), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 256 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 37 residues processed: 294 average time/residue: 2.0424 time to fit residues: 723.3451 Evaluate side-chains 288 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 31 residues processed: 6 average time/residue: 1.8271 time to fit residues: 17.6677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.7980 chunk 332 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 323 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 322 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 29724 Z= 0.145 Angle : 0.513 11.420 40476 Z= 0.263 Chirality : 0.048 1.425 4448 Planarity : 0.003 0.041 5232 Dihedral : 6.187 83.784 3932 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.23 % Favored : 97.66 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3588 helix: 2.49 (0.19), residues: 764 sheet: -0.01 (0.15), residues: 1168 loop : -0.48 (0.16), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 271 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 33 residues processed: 302 average time/residue: 2.0838 time to fit residues: 768.6606 Evaluate side-chains 280 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 247 time to evaluate : 3.464 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 2 average time/residue: 1.9950 time to fit residues: 9.3807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 3.9990 chunk 341 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 358 optimal weight: 0.8980 chunk 330 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 29 optimal weight: 0.0770 chunk 220 optimal weight: 0.1980 chunk 175 optimal weight: 4.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 29724 Z= 0.169 Angle : 0.526 11.472 40476 Z= 0.270 Chirality : 0.048 1.425 4448 Planarity : 0.004 0.046 5232 Dihedral : 6.197 84.419 3932 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.68 % Favored : 97.21 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3588 helix: 2.45 (0.19), residues: 764 sheet: 0.04 (0.15), residues: 1136 loop : -0.48 (0.15), residues: 1688 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 246 time to evaluate : 4.883 Fit side-chains outliers start: 31 outliers final: 29 residues processed: 277 average time/residue: 2.0242 time to fit residues: 681.0106 Evaluate side-chains 272 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 3.481 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 4.3497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 293 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.151913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.131561 restraints weight = 111732.248| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.74 r_work: 0.3823 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.3786 rms_B_bonded: 1.83 restraints_weight: 0.1250 r_work: 0.3762 rms_B_bonded: 2.18 restraints_weight: 0.0625 r_work: 0.3733 rms_B_bonded: 2.70 restraints_weight: 0.0312 r_work: 0.3696 rms_B_bonded: 3.45 restraints_weight: 0.0156 r_work: 0.3649 rms_B_bonded: 4.51 restraints_weight: 0.0078 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 29724 Z= 0.150 Angle : 0.508 11.410 40476 Z= 0.260 Chirality : 0.048 1.420 4448 Planarity : 0.003 0.056 5232 Dihedral : 6.067 84.434 3932 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.31 % Favored : 97.58 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: 0.55 (0.14), residues: 3588 helix: 2.56 (0.19), residues: 764 sheet: 0.03 (0.15), residues: 1164 loop : -0.37 (0.16), residues: 1660 =============================================================================== Job complete usr+sys time: 13430.91 seconds wall clock time: 231 minutes 46.33 seconds (13906.33 seconds total)