Starting phenix.real_space_refine (version: dev) on Sat May 14 05:52:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/05_2022/7b70_12063_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/05_2022/7b70_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_12063/05_2022/7b70_12063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/05_2022/7b70_12063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/05_2022/7b70_12063_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/05_2022/7b70_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 10, 'TRANS': 207, 'PCIS': 1} 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: {'PTRANS': 20, 'CIS': 1, 'TRANS': 592} Chain breaks: 4 Time building chain proxies: 9.37, per 1000 atoms: 0.55 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: 7.29 Conformation dependent library (CDL) restraints added in 2.4 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: 0.70 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: 5.01 Time building geometry restraints manager: 7.82 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 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. 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.440 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.150 Process input model: 46.200 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 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 : 1.129 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 : 43.42 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 : 2.092 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: 0.3796 time to fit residues: 142.0054 Evaluate side-chains 127 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 2.181 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2381 time to fit residues: 8.1817 ------------------------------------------------------------------------------- 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 ** 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 48 ASN G 78 GLN ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 17436 Z= 0.262 Angle : 0.824 12.670 23579 Z= 0.426 Chirality : 0.050 0.723 2650 Planarity : 0.006 0.085 3009 Dihedral : 6.816 82.215 2305 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 32.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.81 (0.17), residues: 2082 helix: -0.32 (0.15), residues: 1071 sheet: -1.37 (0.35), residues: 218 loop : -2.32 (0.21), residues: 793 *********************** 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 168 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 161 average time/residue: 0.3068 time to fit residues: 75.4652 Evaluate side-chains 130 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 2.243 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.1748 time to fit residues: 7.6394 ------------------------------------------------------------------------------- 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: 6.9990 chunk 57 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 201 optimal weight: 0.5980 chunk 166 optimal weight: 0.6980 chunk 184 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 22 ASN ** 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 38 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 17436 Z= 0.221 Angle : 0.751 13.021 23579 Z= 0.382 Chirality : 0.045 0.310 2650 Planarity : 0.005 0.070 3009 Dihedral : 6.378 79.734 2305 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 30.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.74 % Favored : 91.21 % Rotamer Outliers : 2.31 % 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: -1.42 (0.18), residues: 2082 helix: 0.04 (0.15), residues: 1063 sheet: -1.27 (0.35), residues: 224 loop : -2.16 (0.21), residues: 795 *********************** 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 169 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 126 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 17 residues processed: 160 average time/residue: 0.2977 time to fit residues: 74.9598 Evaluate side-chains 128 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 2.091 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1854 time to fit residues: 8.4947 ------------------------------------------------------------------------------- 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: 6.9990 chunk 140 optimal weight: 40.0000 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 89 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 198 optimal weight: 0.0670 chunk 97 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 51 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 33 ASN 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** J 338 ASN ** J 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 17436 Z= 0.196 Angle : 0.706 13.723 23579 Z= 0.360 Chirality : 0.043 0.201 2650 Planarity : 0.005 0.069 3009 Dihedral : 6.085 76.318 2305 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer Outliers : 2.47 % 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: -1.20 (0.18), residues: 2082 helix: 0.23 (0.15), residues: 1071 sheet: -1.14 (0.35), residues: 224 loop : -2.09 (0.22), residues: 787 *********************** 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 169 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 123 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 13 residues processed: 161 average time/residue: 0.2765 time to fit residues: 69.7380 Evaluate side-chains 122 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 2.352 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1912 time to fit residues: 7.2778 ------------------------------------------------------------------------------- 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: 4.9990 chunk 112 optimal weight: 0.0170 chunk 2 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** 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 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 17436 Z= 0.213 Angle : 0.728 13.373 23579 Z= 0.366 Chirality : 0.044 0.305 2650 Planarity : 0.005 0.068 3009 Dihedral : 5.925 70.544 2305 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.31 % Favored : 91.64 % Rotamer Outliers : 1.98 % 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: -1.10 (0.18), residues: 2082 helix: 0.34 (0.15), residues: 1073 sheet: -1.12 (0.36), residues: 218 loop : -2.07 (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 152 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 11 residues processed: 143 average time/residue: 0.2723 time to fit residues: 63.4268 Evaluate side-chains 119 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1723 time to fit residues: 6.4889 ------------------------------------------------------------------------------- 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: 10.0000 chunk 178 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 198 optimal weight: 8.9990 chunk 164 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 ** D 52 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 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 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 521 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 17436 Z= 0.250 Angle : 0.753 13.398 23579 Z= 0.379 Chirality : 0.044 0.258 2650 Planarity : 0.005 0.099 3009 Dihedral : 5.927 63.823 2305 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 31.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.36 % Favored : 91.59 % Rotamer Outliers : 2.14 % 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: -1.12 (0.18), residues: 2082 helix: 0.33 (0.15), residues: 1072 sheet: -1.35 (0.34), residues: 218 loop : -2.03 (0.21), residues: 792 *********************** 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 155 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 115 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 10 residues processed: 148 average time/residue: 0.2764 time to fit residues: 64.8849 Evaluate side-chains 115 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 2.120 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2181 time to fit residues: 6.5230 ------------------------------------------------------------------------------- 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: 7.9990 chunk 22 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 144 optimal weight: 0.0370 chunk 112 optimal weight: 6.9990 chunk 166 optimal weight: 0.2980 chunk 110 optimal weight: 5.9990 chunk 197 optimal weight: 0.0570 chunk 123 optimal weight: 0.1980 chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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** C 99 GLN ** 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** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.4803 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= 0.189 Angle : 0.756 14.036 23579 Z= 0.374 Chirality : 0.044 0.248 2650 Planarity : 0.004 0.059 3009 Dihedral : 5.703 59.235 2305 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 92.99 % Rotamer Outliers : 1.02 % 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: 0.43 (0.15), residues: 1072 sheet: -1.31 (0.34), residues: 220 loop : -1.92 (0.22), residues: 790 *********************** 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 137 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 2.106 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: 19 outliers final: 10 residues processed: 135 average time/residue: 0.2984 time to fit residues: 62.9475 Evaluate side-chains 120 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 2.127 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1721 time to fit residues: 5.9547 ------------------------------------------------------------------------------- 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: 2.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 179 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** 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** ** 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** ** E 88 ASN ** 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 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 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 414 GLN ** J 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 17436 Z= 0.277 Angle : 0.808 14.580 23579 Z= 0.406 Chirality : 0.046 0.291 2650 Planarity : 0.005 0.061 3009 Dihedral : 5.807 49.442 2305 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.45 % Favored : 91.50 % Rotamer Outliers : 1.29 % 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: -1.08 (0.18), residues: 2082 helix: 0.41 (0.15), residues: 1065 sheet: -1.45 (0.34), residues: 224 loop : -2.01 (0.21), residues: 793 *********************** 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 131 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 126 average time/residue: 0.2790 time to fit residues: 56.7048 Evaluate side-chains 114 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 2.127 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1629 time to fit residues: 5.8405 ------------------------------------------------------------------------------- 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: 1.9990 chunk 172 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 145 GLN ** 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** ** 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** ** 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: 0.6762 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 17436 Z= 0.206 Angle : 0.783 15.973 23579 Z= 0.386 Chirality : 0.045 0.255 2650 Planarity : 0.004 0.052 3009 Dihedral : 5.685 47.975 2305 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 29.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer Outliers : 0.97 % 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: -0.99 (0.18), residues: 2082 helix: 0.45 (0.16), residues: 1067 sheet: -1.43 (0.34), residues: 220 loop : -1.93 (0.22), residues: 795 *********************** 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 133 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 127 average time/residue: 0.2744 time to fit residues: 55.4658 Evaluate side-chains 115 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 2.231 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2005 time to fit residues: 5.4162 ------------------------------------------------------------------------------- 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: 0.5980 chunk 118 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** ** A 145 GLN ** 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** H 74 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** ** 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: 0.6745 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 17436 Z= 0.197 Angle : 0.789 16.563 23579 Z= 0.387 Chirality : 0.045 0.374 2650 Planarity : 0.004 0.055 3009 Dihedral : 5.591 47.361 2305 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 27.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.83 % Favored : 92.12 % 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: -0.98 (0.18), residues: 2082 helix: 0.46 (0.16), residues: 1067 sheet: -1.43 (0.35), residues: 212 loop : -1.91 (0.21), residues: 803 ********************** 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 122 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 121 average time/residue: 0.2763 time to fit residues: 54.2082 Evaluate side-chains 112 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1518 time to fit residues: 3.7454 ------------------------------------------------------------------------------- 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: 0.0050 chunk 49 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** 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** ** 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** E 88 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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** G 107 ASN H 33 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 229 GLN ** 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 = 0.4212 r_free = 0.4212 target = 0.053345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.037814 restraints weight = 249209.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.037617 restraints weight = 171926.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.038058 restraints weight = 137700.410| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 17436 Z= 0.328 Angle : 0.877 14.498 23579 Z= 0.441 Chirality : 0.048 0.331 2650 Planarity : 0.006 0.064 3009 Dihedral : 5.938 47.231 2305 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 39.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.98 % Favored : 90.97 % 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: -1.41 (0.18), residues: 2082 helix: 0.11 (0.15), residues: 1072 sheet: -1.72 (0.34), residues: 215 loop : -2.12 (0.21), residues: 795 =============================================================================== Job complete usr+sys time: 3310.88 seconds wall clock time: 61 minutes 48.88 seconds (3708.88 seconds total)