Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 13:19:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfh_25872/10_2023/7tfh_25872_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfh_25872/10_2023/7tfh_25872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfh_25872/10_2023/7tfh_25872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfh_25872/10_2023/7tfh_25872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfh_25872/10_2023/7tfh_25872_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfh_25872/10_2023/7tfh_25872_updated.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 370 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Se 18 7.20 5 P 77 5.49 5 Mg 4 5.21 5 S 86 5.16 5 C 14225 2.51 5 N 3895 2.21 5 O 4526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 376": "OE1" <-> "OE2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "G PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 22831 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4925 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 24, 'TRANS': 603} Chain breaks: 3 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2615 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2622 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2694 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "G" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2014 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "I" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "K" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.02, per 1000 atoms: 0.53 Number of scatterers: 22831 At special positions: 0 Unit cell: (125.028, 146.556, 139.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Se 18 33.99 S 86 16.00 P 77 15.00 Mg 4 11.99 O 4526 8.00 N 3895 7.00 C 14225 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: 9.55 Conformation dependent library (CDL) restraints added in 3.3 seconds 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 20 sheets defined 45.9% alpha, 12.6% beta 25 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 10.24 Creating SS restraints... Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.502A pdb=" N LYS A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 removed outlier: 4.121A pdb=" N TYR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.846A pdb=" N LYS A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.892A pdb=" N GLN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 241 through 280 removed outlier: 3.946A pdb=" N GLU A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.870A pdb=" N PHE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 514 through 526 removed outlier: 3.791A pdb=" N THR A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 566 through 571 removed outlier: 3.806A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 571' Processing helix chain 'A' and resid 574 through 594 removed outlier: 4.312A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 610 through 631 Processing helix chain 'A' and resid 638 through 656 removed outlier: 3.549A pdb=" N LEU A 641 " --> pdb=" O TRP A 638 " (cutoff:3.500A) Proline residue: A 642 - end of helix removed outlier: 3.579A pdb=" N SER A 648 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL A 650 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR A 651 " --> pdb=" O SER A 648 " (cutoff:3.500A) Proline residue: A 652 - end of helix removed outlier: 3.585A pdb=" N LYS A 655 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 689 Processing helix chain 'A' and resid 698 through 703 removed outlier: 3.629A pdb=" N ARG A 702 " --> pdb=" O LYS A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 713 removed outlier: 3.871A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 719 Processing helix chain 'A' and resid 721 through 734 removed outlier: 3.615A pdb=" N ALA A 724 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER A 726 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 727 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 728 " --> pdb=" O ILE A 725 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 733 " --> pdb=" O GLU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.578A pdb=" N ASP A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 746 " --> pdb=" O TRP A 742 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 764 through 776 removed outlier: 3.521A pdb=" N GLY A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 770 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 771 " --> pdb=" O LYS A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 87 through 98 removed outlier: 4.084A pdb=" N GLN B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.808A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 75 through 78 No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.019A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.847A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.091A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.140A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.790A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 333 removed outlier: 3.744A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 44 through 54 removed outlier: 3.898A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 103 through 115 removed outlier: 4.005A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 removed outlier: 4.387A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 198 through 208 Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 297 through 308 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.758A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 20 through 32 removed outlier: 3.972A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 102 through 116 removed outlier: 3.885A pdb=" N ASP E 105 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E 107 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL E 108 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU E 111 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU E 112 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 113 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 150 through 160 removed outlier: 4.170A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 338 through 353 Processing helix chain 'F' and resid 12 through 22 removed outlier: 4.184A pdb=" N GLY F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 73 through 81 removed outlier: 4.539A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 209 through 218 removed outlier: 4.375A pdb=" N GLY F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.555A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 79 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 209 through 221 removed outlier: 3.863A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER G 219 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 19 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 72 through 81 removed outlier: 4.081A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 209 through 218 removed outlier: 3.773A pdb=" N LYS H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 165 removed outlier: 7.407A pdb=" N VAL A 198 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS A 219 " --> pdb=" O VAL A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.315A pdb=" N LEU A 451 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU A 351 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU A 453 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP A 424 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN A 377 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 599 through 601 Processing sheet with id= D, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.175A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.649A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 185 through 189 removed outlier: 6.371A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 186 through 190 removed outlier: 3.865A pdb=" N GLY E 43 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 68 through 76 removed outlier: 3.601A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 66 through 68 removed outlier: 4.102A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 46 through 49 removed outlier: 3.662A pdb=" N GLY F 244 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 236 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS F 196 " --> pdb=" O SER F 138 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 98 through 104 removed outlier: 3.592A pdb=" N ALA F 112 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 157 through 160 Processing sheet with id= M, first strand: chain 'F' and resid 167 through 172 Processing sheet with id= N, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.909A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.812A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 66 through 68 removed outlier: 4.238A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 157 through 160 Processing sheet with id= R, first strand: chain 'G' and resid 166 through 172 Processing sheet with id= S, first strand: chain 'H' and resid 111 through 117 removed outlier: 4.361A pdb=" N LEU H 88 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS H 5 " --> pdb=" O GLU H 59 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU H 59 " --> pdb=" O LYS H 5 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 27 through 30 removed outlier: 4.100A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN H 38 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE H 237 " --> pdb=" O PHE H 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU H 236 " --> pdb=" O ARG H 228 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN H 238 " --> pdb=" O GLY H 226 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU H 139 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 136 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 138 " --> pdb=" O LYS H 196 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS H 196 " --> pdb=" O SER H 138 " (cutoff:3.500A) 917 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 8.59 Time building geometry restraints manager: 10.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 7500 1.37 - 1.52: 8078 1.52 - 1.67: 7579 1.67 - 1.82: 124 1.82 - 1.97: 40 Bond restraints: 23321 Sorted by residual: bond pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" C4 ADP E 500 " pdb=" C5 ADP E 500 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" CG ARG E 106 " pdb=" CD ARG E 106 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB PRO G 184 " pdb=" CG PRO G 184 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 1.00e+00 bond pdb=" CB GLN E 32 " pdb=" CG GLN E 32 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.28e-01 ... (remaining 23316 not shown) Histogram of bond angle deviations from ideal: 97.19 - 105.00: 554 105.00 - 112.81: 13107 112.81 - 120.63: 10105 120.63 - 128.44: 7858 128.44 - 136.25: 156 Bond angle restraints: 31780 Sorted by residual: angle pdb=" CG ARG D 115 " pdb=" CD ARG D 115 " pdb=" NE ARG D 115 " ideal model delta sigma weight residual 112.00 118.24 -6.24 2.20e+00 2.07e-01 8.05e+00 angle pdb=" C LYS D 80 " pdb=" N GLU D 81 " pdb=" CA GLU D 81 " ideal model delta sigma weight residual 122.65 118.53 4.12 1.60e+00 3.91e-01 6.63e+00 angle pdb=" C ASP C 223 " pdb=" N GLU C 224 " pdb=" CA GLU C 224 " ideal model delta sigma weight residual 122.61 126.46 -3.85 1.56e+00 4.11e-01 6.09e+00 angle pdb=" N GLU A 236 " pdb=" CA GLU A 236 " pdb=" CB GLU A 236 " ideal model delta sigma weight residual 113.65 110.08 3.57 1.47e+00 4.63e-01 5.90e+00 angle pdb=" C SER A 334 " pdb=" N PHE A 335 " pdb=" CA PHE A 335 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.74e+00 ... (remaining 31775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.02: 13376 30.02 - 60.04: 663 60.04 - 90.05: 34 90.05 - 120.07: 1 120.07 - 150.09: 2 Dihedral angle restraints: 14076 sinusoidal: 6150 harmonic: 7926 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -171.67 111.67 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 82.36 -150.09 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" CA LEU B 103 " pdb=" C LEU B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 14073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2915 0.046 - 0.092: 607 0.092 - 0.138: 169 0.138 - 0.184: 3 0.184 - 0.230: 4 Chirality restraints: 3698 Sorted by residual: chirality pdb=" CB ILE H 111 " pdb=" CA ILE H 111 " pdb=" CG1 ILE H 111 " pdb=" CG2 ILE H 111 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU B 67 " pdb=" CB LEU B 67 " pdb=" CD1 LEU B 67 " pdb=" CD2 LEU B 67 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE B 86 " pdb=" CA ILE B 86 " pdb=" CG1 ILE B 86 " pdb=" CG2 ILE B 86 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3695 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 97 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO E 98 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 353 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 354 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 232 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO B 233 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.028 5.00e-02 4.00e+02 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 279 2.63 - 3.20: 20065 3.20 - 3.77: 36241 3.77 - 4.33: 50495 4.33 - 4.90: 82241 Nonbonded interactions: 189321 Sorted by model distance: nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.066 2.170 nonbonded pdb=" OG1 THR A 360 " pdb="MG MG A 902 " model vdw 2.074 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.078 2.170 nonbonded pdb=" O3G AGS A 901 " pdb="MG MG A 902 " model vdw 2.080 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.095 2.170 ... (remaining 189316 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 'F' and resid 1 through 254) selection = (chain 'G' and resid 1 through 254) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 14.400 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 66.970 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.003 0.050 23321 Z= 0.176 Angle : 0.563 8.282 31780 Z= 0.288 Chirality : 0.040 0.230 3698 Planarity : 0.004 0.120 3814 Dihedral : 15.931 150.091 8920 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.04 % Allowed : 0.29 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2693 helix: 0.98 (0.15), residues: 1275 sheet: -0.35 (0.25), residues: 505 loop : -0.89 (0.20), residues: 913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.3494 time to fit residues: 200.9977 Evaluate side-chains 294 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 2.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 160 optimal weight: 0.0020 chunk 249 optimal weight: 4.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 140 ASN C 202 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 238 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23321 Z= 0.240 Angle : 0.536 7.231 31780 Z= 0.278 Chirality : 0.040 0.147 3698 Planarity : 0.004 0.102 3814 Dihedral : 14.999 152.057 3567 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.96 % Allowed : 8.70 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2693 helix: 1.12 (0.15), residues: 1284 sheet: -0.31 (0.24), residues: 510 loop : -0.87 (0.20), residues: 899 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 317 time to evaluate : 2.601 Fit side-chains outliers start: 23 outliers final: 21 residues processed: 325 average time/residue: 0.3560 time to fit residues: 180.6325 Evaluate side-chains 314 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 293 time to evaluate : 2.701 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2320 time to fit residues: 12.7049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 170 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 140 ASN C 167 GLN C 202 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23321 Z= 0.201 Angle : 0.499 7.260 31780 Z= 0.257 Chirality : 0.039 0.158 3698 Planarity : 0.004 0.098 3814 Dihedral : 15.037 151.333 3567 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.58 % Allowed : 11.82 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2693 helix: 1.23 (0.15), residues: 1285 sheet: -0.20 (0.24), residues: 497 loop : -0.86 (0.20), residues: 911 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 305 time to evaluate : 2.566 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 316 average time/residue: 0.3733 time to fit residues: 183.5304 Evaluate side-chains 292 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 284 time to evaluate : 2.631 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2138 time to fit residues: 6.7228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 3.9990 chunk 188 optimal weight: 0.4980 chunk 129 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 251 optimal weight: 0.6980 chunk 265 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 140 ASN C 202 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23321 Z= 0.186 Angle : 0.495 7.467 31780 Z= 0.255 Chirality : 0.039 0.167 3698 Planarity : 0.004 0.090 3814 Dihedral : 15.025 151.134 3567 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.12 % Allowed : 12.74 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2693 helix: 1.30 (0.15), residues: 1283 sheet: -0.19 (0.24), residues: 497 loop : -0.83 (0.20), residues: 913 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 298 time to evaluate : 2.682 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 311 average time/residue: 0.3721 time to fit residues: 180.9630 Evaluate side-chains 297 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 282 time to evaluate : 2.626 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2190 time to fit residues: 9.7704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 0.3980 chunk 150 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 183 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 326 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 140 ASN C 202 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23321 Z= 0.226 Angle : 0.507 7.364 31780 Z= 0.261 Chirality : 0.039 0.164 3698 Planarity : 0.004 0.090 3814 Dihedral : 15.092 151.571 3567 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.87 % Allowed : 14.74 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2693 helix: 1.26 (0.15), residues: 1287 sheet: -0.17 (0.24), residues: 501 loop : -0.78 (0.20), residues: 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 307 time to evaluate : 3.300 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 323 average time/residue: 0.3647 time to fit residues: 182.8977 Evaluate side-chains 303 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 291 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2031 time to fit residues: 8.0251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 266 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 140 ASN C 202 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23321 Z= 0.281 Angle : 0.541 7.593 31780 Z= 0.277 Chirality : 0.041 0.175 3698 Planarity : 0.004 0.087 3814 Dihedral : 15.192 151.714 3567 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.08 % Allowed : 15.78 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2693 helix: 1.17 (0.15), residues: 1289 sheet: -0.15 (0.24), residues: 499 loop : -0.80 (0.20), residues: 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 302 time to evaluate : 2.423 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 317 average time/residue: 0.3705 time to fit residues: 181.7499 Evaluate side-chains 312 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 295 time to evaluate : 2.980 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2205 time to fit residues: 10.7988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 684 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 140 ASN C 202 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN G 64 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23321 Z= 0.287 Angle : 0.543 8.157 31780 Z= 0.278 Chirality : 0.041 0.188 3698 Planarity : 0.004 0.085 3814 Dihedral : 15.238 151.533 3567 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.54 % Allowed : 16.49 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2693 helix: 1.15 (0.15), residues: 1281 sheet: -0.17 (0.24), residues: 499 loop : -0.82 (0.20), residues: 913 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 300 time to evaluate : 2.857 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 311 average time/residue: 0.3676 time to fit residues: 177.2378 Evaluate side-chains 302 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 293 time to evaluate : 2.473 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2073 time to fit residues: 7.1365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 158 optimal weight: 0.0570 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 146 GLN B 148 ASN B 317 HIS C 140 ASN C 202 ASN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23321 Z= 0.192 Angle : 0.513 10.029 31780 Z= 0.263 Chirality : 0.039 0.179 3698 Planarity : 0.004 0.087 3814 Dihedral : 15.157 150.869 3567 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.50 % Allowed : 17.11 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2693 helix: 1.30 (0.15), residues: 1277 sheet: -0.08 (0.24), residues: 509 loop : -0.79 (0.20), residues: 907 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 295 time to evaluate : 2.982 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 299 average time/residue: 0.3740 time to fit residues: 172.9709 Evaluate side-chains 295 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 286 time to evaluate : 2.798 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2665 time to fit residues: 7.8559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 3.9990 chunk 253 optimal weight: 0.2980 chunk 231 optimal weight: 0.6980 chunk 246 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN B 148 ASN B 317 HIS C 77 ASN C 140 ASN C 202 ASN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23321 Z= 0.208 Angle : 0.519 9.126 31780 Z= 0.267 Chirality : 0.039 0.186 3698 Planarity : 0.004 0.087 3814 Dihedral : 15.130 151.197 3567 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.29 % Allowed : 17.49 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2693 helix: 1.30 (0.15), residues: 1283 sheet: -0.07 (0.24), residues: 501 loop : -0.76 (0.20), residues: 909 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 294 time to evaluate : 2.660 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 298 average time/residue: 0.3731 time to fit residues: 174.0093 Evaluate side-chains 295 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 290 time to evaluate : 2.409 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2096 time to fit residues: 5.4406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 7.9990 chunk 159 optimal weight: 0.3980 chunk 123 optimal weight: 0.9990 chunk 181 optimal weight: 0.0870 chunk 273 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 140 ASN C 202 ASN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23321 Z= 0.177 Angle : 0.512 10.562 31780 Z= 0.262 Chirality : 0.039 0.193 3698 Planarity : 0.004 0.086 3814 Dihedral : 15.084 151.024 3567 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.29 % Allowed : 17.82 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2693 helix: 1.40 (0.15), residues: 1275 sheet: -0.02 (0.24), residues: 509 loop : -0.74 (0.20), residues: 909 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 298 time to evaluate : 2.433 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 301 average time/residue: 0.3680 time to fit residues: 172.6268 Evaluate side-chains 291 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 287 time to evaluate : 2.749 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2131 time to fit residues: 5.2396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 201 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 27 optimal weight: 0.0000 chunk 40 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS C 140 ASN C 202 ASN D 243 GLN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** G 27 ASN ** 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 = 0.4089 r_free = 0.4089 target = 0.151361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110242 restraints weight = 31887.183| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.07 r_work: 0.3343 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23321 Z= 0.192 Angle : 0.515 10.517 31780 Z= 0.263 Chirality : 0.039 0.184 3698 Planarity : 0.004 0.086 3814 Dihedral : 15.078 151.318 3567 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.12 % Allowed : 17.99 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2693 helix: 1.41 (0.15), residues: 1277 sheet: 0.01 (0.24), residues: 500 loop : -0.72 (0.20), residues: 916 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5251.09 seconds wall clock time: 96 minutes 27.56 seconds (5787.56 seconds total)