Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 08:24:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/04_2023/7b70_12063_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/04_2023/7b70_12063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/04_2023/7b70_12063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/04_2023/7b70_12063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/04_2023/7b70_12063_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/04_2023/7b70_12063_neut.pdb" } resolution = 4.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 10934 2.51 5 N 2914 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 31": "NH1" <-> "NH2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "F TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "G ARG 52": "NH1" <-> "NH2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "I ARG 358": "NH1" <-> "NH2" Residue "I GLU 374": "OE1" <-> "OE2" Residue "I ARG 429": "NH1" <-> "NH2" Residue "I TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 508": "NH1" <-> "NH2" Residue "I GLU 537": "OE1" <-> "OE2" Residue "I ASP 539": "OD1" <-> "OD2" Residue "I TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J GLU 182": "OE1" <-> "OE2" Residue "J ARG 363": "NH1" <-> "NH2" Residue "J GLU 419": "OE1" <-> "OE2" Residue "J TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 446": "NH1" <-> "NH2" Residue "J GLU 514": "OE1" <-> "OE2" Residue "J PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 699": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17084 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "B" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "C" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1204 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1741 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207} Chain: "E" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1177 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "F" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1333 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "G" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1363 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1089 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "I" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1710 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain breaks: 1 Chain: "J" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4904 Classifications: {'peptide': 614} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 592} Chain breaks: 4 Time building chain proxies: 9.02, per 1000 atoms: 0.53 Number of scatterers: 17084 At special positions: 0 Unit cell: (204.793, 283.946, 113.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 3141 8.00 N 2914 7.00 C 10934 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: 8.02 Conformation dependent library (CDL) restraints added in 2.5 seconds 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 53.2% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 16 through 33 removed outlier: 3.783A pdb=" N LEU A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 62 removed outlier: 4.250A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 126 through 140 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.318A pdb=" N PHE B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.699A pdb=" N ARG B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 removed outlier: 4.126A pdb=" N PHE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 104 through 121 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 166 through 182 Processing helix chain 'D' and resid 195 through 211 Processing helix chain 'E' and resid 26 through 55 removed outlier: 3.606A pdb=" N HIS E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 110 removed outlier: 3.890A pdb=" N ASN E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'F' and resid 32 through 50 Processing helix chain 'F' and resid 52 through 78 removed outlier: 4.041A pdb=" N ARG F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.623A pdb=" N THR F 132 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 161 Processing helix chain 'F' and resid 181 through 191 Processing helix chain 'G' and resid 13 through 32 removed outlier: 3.554A pdb=" N LEU G 17 " --> pdb=" O ASN G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 61 removed outlier: 3.552A pdb=" N MET G 51 " --> pdb=" O TYR G 47 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG G 52 " --> pdb=" O ASN G 48 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 84 removed outlier: 3.605A pdb=" N THR G 72 " --> pdb=" O GLU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 120 removed outlier: 3.705A pdb=" N THR G 120 " --> pdb=" O PRO G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 126 through 139 Processing helix chain 'G' and resid 150 through 154 removed outlier: 3.712A pdb=" N GLY G 154 " --> pdb=" O GLN G 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.884A pdb=" N VAL H 95 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 138 Processing helix chain 'I' and resid 356 through 385 Proline residue: I 371 - end of helix Processing helix chain 'I' and resid 425 through 436 Processing helix chain 'I' and resid 440 through 453 Processing helix chain 'I' and resid 460 through 479 removed outlier: 4.142A pdb=" N TYR I 464 " --> pdb=" O ALA I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 492 Processing helix chain 'I' and resid 493 through 500 removed outlier: 3.519A pdb=" N THR I 498 " --> pdb=" O VAL I 494 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL I 499 " --> pdb=" O CYS I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 520 Processing helix chain 'I' and resid 522 through 535 removed outlier: 3.701A pdb=" N VAL I 526 " --> pdb=" O LEU I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 539 through 557 removed outlier: 3.557A pdb=" N THR I 556 " --> pdb=" O CYS I 552 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN I 557 " --> pdb=" O PHE I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 578 removed outlier: 3.519A pdb=" N LEU I 570 " --> pdb=" O PHE I 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 598 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 33 through 46 removed outlier: 4.264A pdb=" N SER J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU J 44 " --> pdb=" O PHE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 94 removed outlier: 3.565A pdb=" N HIS J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 135 removed outlier: 5.248A pdb=" N GLU J 133 " --> pdb=" O ASN J 129 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG J 134 " --> pdb=" O THR J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 169 Processing helix chain 'J' and resid 180 through 215 removed outlier: 5.077A pdb=" N GLY J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 239 Processing helix chain 'J' and resid 243 through 259 Processing helix chain 'J' and resid 265 through 287 removed outlier: 4.178A pdb=" N ILE J 269 " --> pdb=" O ASN J 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 308 removed outlier: 3.859A pdb=" N VAL J 308 " --> pdb=" O HIS J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 339 Processing helix chain 'J' and resid 341 through 347 removed outlier: 3.841A pdb=" N GLN J 346 " --> pdb=" O ALA J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 374 removed outlier: 4.324A pdb=" N HIS J 353 " --> pdb=" O GLY J 349 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS J 354 " --> pdb=" O ILE J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 422 Processing helix chain 'J' and resid 425 through 442 removed outlier: 4.036A pdb=" N ILE J 429 " --> pdb=" O SER J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 463 Processing helix chain 'J' and resid 464 through 483 removed outlier: 3.605A pdb=" N ALA J 468 " --> pdb=" O ASP J 464 " (cutoff:3.500A) Proline residue: J 477 - end of helix Processing helix chain 'J' and resid 484 through 503 removed outlier: 3.883A pdb=" N THR J 489 " --> pdb=" O THR J 485 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS J 494 " --> pdb=" O ASP J 490 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 518 removed outlier: 3.725A pdb=" N LEU J 518 " --> pdb=" O GLU J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 539 Processing helix chain 'J' and resid 550 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.731A pdb=" N VAL A 163 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 103 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 161 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A 160 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 164 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 145 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 166 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A 143 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.597A pdb=" N TYR B 86 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.908A pdb=" N ILE C 8 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR C 18 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 6 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN C 5 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 64 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR C 63 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU D 135 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 143 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 8 " --> pdb=" O ILE D 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32 removed outlier: 4.071A pdb=" N LYS D 30 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 96 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 65 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER D 99 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU D 63 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 71 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 40 through 43 Processing sheet with id=AA6, first strand: chain 'E' and resid 15 through 20 removed outlier: 3.583A pdb=" N TYR E 5 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 83 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS E 86 " --> pdb=" O PHE E 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 110 through 113 removed outlier: 3.509A pdb=" N ILE F 124 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 99 through 100 removed outlier: 3.505A pdb=" N PHE G 100 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 99 through 100 removed outlier: 3.505A pdb=" N PHE G 100 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU G 159 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLU G 142 " --> pdb=" O VAL G 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.677A pdb=" N TYR H 61 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY H 70 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU H 59 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL H 72 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU H 57 " --> pdb=" O VAL H 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 55 through 56 removed outlier: 4.271A pdb=" N VAL J 99 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL J 101 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU J 102 " --> pdb=" O CYS J 139 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL J 141 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N PHE J 176 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU J 140 " --> pdb=" O PHE J 176 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU J 178 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU J 142 " --> pdb=" O LEU J 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 602 through 603 removed outlier: 4.495A pdb=" N VAL J 602 " --> pdb=" O TYR J 678 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR J 678 " --> pdb=" O VAL J 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 900 hydrogen bonds defined for protein. 2634 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: 5.11 Time building geometry restraints manager: 8.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4504 1.33 - 1.45: 3567 1.45 - 1.58: 9213 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 17436 Sorted by residual: bond pdb=" N VAL H 39 " pdb=" CA VAL H 39 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.08e-02 8.57e+03 1.59e+01 bond pdb=" C GLU F 127 " pdb=" N PRO F 128 " ideal model delta sigma weight residual 1.334 1.292 0.042 1.11e-02 8.12e+03 1.41e+01 bond pdb=" N GLN I 557 " pdb=" CA GLN I 557 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.12e+01 bond pdb=" C HIS D 61 " pdb=" N VAL D 62 " ideal model delta sigma weight residual 1.334 1.292 0.041 1.24e-02 6.50e+03 1.11e+01 bond pdb=" C TRP C 115 " pdb=" N THR C 116 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.47e-02 4.63e+03 1.09e+01 ... (remaining 17431 not shown) Histogram of bond angle deviations from ideal: 97.09 - 104.53: 222 104.53 - 111.98: 8294 111.98 - 119.42: 6328 119.42 - 126.87: 8549 126.87 - 134.31: 186 Bond angle restraints: 23579 Sorted by residual: angle pdb=" N GLU H 40 " pdb=" CA GLU H 40 " pdb=" C GLU H 40 " ideal model delta sigma weight residual 112.54 103.73 8.81 1.22e+00 6.72e-01 5.21e+01 angle pdb=" N VAL H 39 " pdb=" CA VAL H 39 " pdb=" C VAL H 39 " ideal model delta sigma weight residual 113.42 105.30 8.12 1.17e+00 7.31e-01 4.81e+01 angle pdb=" N VAL I 569 " pdb=" CA VAL I 569 " pdb=" C VAL I 569 " ideal model delta sigma weight residual 111.00 104.39 6.61 1.09e+00 8.42e-01 3.68e+01 angle pdb=" N LEU H 44 " pdb=" CA LEU H 44 " pdb=" C LEU H 44 " ideal model delta sigma weight residual 113.15 106.07 7.08 1.19e+00 7.06e-01 3.54e+01 angle pdb=" N ILE E 40 " pdb=" CA ILE E 40 " pdb=" C ILE E 40 " ideal model delta sigma weight residual 111.44 104.39 7.05 1.34e+00 5.57e-01 2.76e+01 ... (remaining 23574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9261 17.82 - 35.64: 967 35.64 - 53.46: 229 53.46 - 71.28: 55 71.28 - 89.10: 15 Dihedral angle restraints: 10527 sinusoidal: 4286 harmonic: 6241 Sorted by residual: dihedral pdb=" CA ILE D 214 " pdb=" C ILE D 214 " pdb=" N SER D 215 " pdb=" CA SER D 215 " ideal model delta harmonic sigma weight residual 180.00 140.32 39.68 0 5.00e+00 4.00e-02 6.30e+01 dihedral pdb=" CA ILE F 134 " pdb=" C ILE F 134 " pdb=" N SER F 135 " pdb=" CA SER F 135 " ideal model delta harmonic sigma weight residual 180.00 -141.08 -38.92 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" C VAL H 38 " pdb=" N VAL H 38 " pdb=" CA VAL H 38 " pdb=" CB VAL H 38 " ideal model delta harmonic sigma weight residual -122.00 -137.89 15.89 0 2.50e+00 1.60e-01 4.04e+01 ... (remaining 10524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2231 0.083 - 0.165: 368 0.165 - 0.248: 37 0.248 - 0.331: 8 0.331 - 0.414: 6 Chirality restraints: 2650 Sorted by residual: chirality pdb=" CB ILE F 134 " pdb=" CA ILE F 134 " pdb=" CG1 ILE F 134 " pdb=" CG2 ILE F 134 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CG LEU D 197 " pdb=" CB LEU D 197 " pdb=" CD1 LEU D 197 " pdb=" CD2 LEU D 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA HIS I 567 " pdb=" N HIS I 567 " pdb=" C HIS I 567 " pdb=" CB HIS I 567 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 2647 not shown) Planarity restraints: 3009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 41 " -0.028 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C ALA E 41 " 0.100 2.00e-02 2.50e+03 pdb=" O ALA E 41 " -0.039 2.00e-02 2.50e+03 pdb=" N HIS E 42 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 117 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO A 118 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 136 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO F 137 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO F 137 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 137 " -0.041 5.00e-02 4.00e+02 ... (remaining 3006 not shown) Histogram of nonbonded interaction distances: 0.46 - 1.35: 11 1.35 - 2.24: 78 2.24 - 3.13: 15948 3.13 - 4.01: 49640 4.01 - 4.90: 85044 Warning: very small nonbonded interaction distances. Nonbonded interactions: 150721 Sorted by model distance: nonbonded pdb=" NE2 HIS H 31 " pdb=" N ILE J 487 " model vdw 0.463 3.200 nonbonded pdb=" CE1 HIS H 31 " pdb=" CA ILE J 487 " model vdw 0.862 3.690 nonbonded pdb=" CB ALA H 34 " pdb=" CZ2 TRP J 484 " model vdw 0.934 3.760 nonbonded pdb=" CA ALA H 34 " pdb=" CH2 TRP J 484 " model vdw 1.025 3.770 nonbonded pdb=" CE1 HIS H 31 " pdb=" N ILE J 487 " model vdw 1.048 3.340 ... (remaining 150716 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 'G' and resid 9 through 173) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 15.470 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 45.460 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.088 17436 Z= 0.502 Angle : 1.130 14.570 23579 Z= 0.691 Chirality : 0.064 0.414 2650 Planarity : 0.006 0.076 3009 Dihedral : 15.939 89.102 6469 Min Nonbonded Distance : 0.463 Molprobity Statistics. All-atom Clashscore : 43.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.91 % Favored : 87.85 % Rotamer Outliers : 4.66 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.17), residues: 2082 helix: -0.89 (0.15), residues: 1038 sheet: -1.65 (0.34), residues: 226 loop : -2.49 (0.21), residues: 818 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 198 time to evaluate : 2.059 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 outliers start: 87 outliers final: 14 residues processed: 269 average time/residue: 0.4081 time to fit residues: 151.0486 Evaluate side-chains 127 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2493 time to fit residues: 8.2483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN E 38 GLN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN G 78 GLN H 93 ASN I 375 HIS I 427 GLN I 504 GLN I 561 HIS ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 ASN ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 17436 Z= 0.263 Angle : 0.810 11.241 23579 Z= 0.421 Chirality : 0.049 0.710 2650 Planarity : 0.005 0.075 3009 Dihedral : 6.770 82.145 2305 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.80 (0.17), residues: 2082 helix: -0.30 (0.15), residues: 1068 sheet: -1.33 (0.35), residues: 223 loop : -2.34 (0.21), residues: 791 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.946 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 outliers start: 28 outliers final: 16 residues processed: 155 average time/residue: 0.3220 time to fit residues: 75.9159 Evaluate side-chains 131 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 2.045 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1785 time to fit residues: 8.0610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 GLN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 17436 Z= 0.233 Angle : 0.747 12.443 23579 Z= 0.384 Chirality : 0.045 0.290 2650 Planarity : 0.005 0.069 3009 Dihedral : 6.368 79.249 2305 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 30.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.65 % Favored : 91.31 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.45 (0.18), residues: 2082 helix: 0.01 (0.15), residues: 1067 sheet: -1.28 (0.35), residues: 224 loop : -2.18 (0.21), residues: 791 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 124 time to evaluate : 2.222 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 outliers start: 48 outliers final: 17 residues processed: 163 average time/residue: 0.2943 time to fit residues: 73.6393 Evaluate side-chains 127 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1580 time to fit residues: 7.6466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 89 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 17436 Z= 0.236 Angle : 0.720 13.462 23579 Z= 0.371 Chirality : 0.044 0.205 2650 Planarity : 0.005 0.070 3009 Dihedral : 6.162 74.237 2305 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 30.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.93 % Favored : 92.03 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.18), residues: 2082 helix: 0.16 (0.15), residues: 1071 sheet: -1.19 (0.35), residues: 218 loop : -2.12 (0.21), residues: 793 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 119 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 17 residues processed: 156 average time/residue: 0.3094 time to fit residues: 75.0197 Evaluate side-chains 127 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.987 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1765 time to fit residues: 8.2426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 17436 Z= 0.205 Angle : 0.720 11.258 23579 Z= 0.363 Chirality : 0.044 0.311 2650 Planarity : 0.005 0.068 3009 Dihedral : 5.988 69.907 2305 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 28.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.97 % Favored : 91.98 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.16 (0.18), residues: 2082 helix: 0.26 (0.15), residues: 1073 sheet: -1.16 (0.36), residues: 218 loop : -2.06 (0.21), residues: 791 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 147 average time/residue: 0.2946 time to fit residues: 67.9467 Evaluate side-chains 125 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 2.213 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1764 time to fit residues: 7.7992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 164 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 17436 Z= 0.192 Angle : 0.710 11.793 23579 Z= 0.358 Chirality : 0.044 0.220 2650 Planarity : 0.004 0.066 3009 Dihedral : 5.853 64.190 2305 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 26.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.49 % Favored : 92.46 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2082 helix: 0.41 (0.15), residues: 1070 sheet: -1.30 (0.35), residues: 218 loop : -2.01 (0.21), residues: 794 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 4 residues processed: 143 average time/residue: 0.2889 time to fit residues: 64.7313 Evaluate side-chains 109 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 2.153 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1646 time to fit residues: 3.9838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 17436 Z= 0.194 Angle : 0.747 13.968 23579 Z= 0.371 Chirality : 0.044 0.285 2650 Planarity : 0.004 0.062 3009 Dihedral : 5.700 57.867 2305 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 27.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.78 % Favored : 92.17 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.98 (0.18), residues: 2082 helix: 0.45 (0.15), residues: 1073 sheet: -1.32 (0.35), residues: 214 loop : -1.96 (0.21), residues: 795 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 136 average time/residue: 0.2962 time to fit residues: 63.5032 Evaluate side-chains 114 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1665 time to fit residues: 5.8629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 134 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 414 GLN ** J 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 17436 Z= 0.188 Angle : 0.752 15.710 23579 Z= 0.371 Chirality : 0.044 0.266 2650 Planarity : 0.004 0.062 3009 Dihedral : 5.608 52.788 2305 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 26.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.89 (0.18), residues: 2082 helix: 0.52 (0.15), residues: 1070 sheet: -1.32 (0.35), residues: 213 loop : -1.89 (0.21), residues: 799 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 122 average time/residue: 0.2992 time to fit residues: 57.6351 Evaluate side-chains 112 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 2.075 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1563 time to fit residues: 4.1243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 17436 Z= 0.189 Angle : 0.756 15.438 23579 Z= 0.374 Chirality : 0.044 0.238 2650 Planarity : 0.004 0.062 3009 Dihedral : 5.564 46.834 2305 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 26.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.90 (0.18), residues: 2082 helix: 0.52 (0.16), residues: 1070 sheet: -1.34 (0.35), residues: 212 loop : -1.89 (0.21), residues: 800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 122 average time/residue: 0.2998 time to fit residues: 57.6521 Evaluate side-chains 111 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2800 time to fit residues: 4.1064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.0050 chunk 118 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17436 Z= 0.183 Angle : 0.777 15.780 23579 Z= 0.380 Chirality : 0.044 0.212 2650 Planarity : 0.004 0.060 3009 Dihedral : 5.501 45.506 2305 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.20 % Favored : 92.75 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.90 (0.18), residues: 2082 helix: 0.49 (0.16), residues: 1069 sheet: -1.34 (0.36), residues: 206 loop : -1.85 (0.21), residues: 807 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 120 average time/residue: 0.2954 time to fit residues: 56.1529 Evaluate side-chains 108 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1643 time to fit residues: 3.5850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN C 99 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 HIS ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.054010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.039652 restraints weight = 245631.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.037017 restraints weight = 187591.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.037379 restraints weight = 147435.117| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.004 0.072 17436 Z= 0.285 Angle : 0.850 18.419 23579 Z= 0.424 Chirality : 0.046 0.294 2650 Planarity : 0.005 0.066 3009 Dihedral : 5.745 45.241 2305 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 35.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.55 % Favored : 91.40 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.17 (0.18), residues: 2082 helix: 0.29 (0.15), residues: 1069 sheet: -1.46 (0.36), residues: 202 loop : -2.01 (0.21), residues: 811 =============================================================================== Job complete usr+sys time: 3380.89 seconds wall clock time: 63 minutes 7.79 seconds (3787.79 seconds total)