Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 08:22:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/04_2023/7tfk_25875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/04_2023/7tfk_25875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/04_2023/7tfk_25875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/04_2023/7tfk_25875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/04_2023/7tfk_25875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/04_2023/7tfk_25875_updated.pdb" } resolution = 3.25 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= -0.001 sd= 0.030 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 220 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: 6 Type Number sf(0) Gaussians P 59 5.49 5 Mg 4 5.21 5 S 68 5.16 5 C 8888 2.51 5 N 2521 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14363 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2862 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain breaks: 2 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2606 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 12, 'TRANS': 316} 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: "I" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "J" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} 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: 8.19, per 1000 atoms: 0.57 Number of scatterers: 14363 At special positions: 0 Unit cell: (87.768, 119.232, 128.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 59 15.00 Mg 4 11.99 O 2823 8.00 N 2521 7.00 C 8888 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.10 Conformation dependent library (CDL) restraints added in 2.3 seconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 5 sheets defined 54.7% alpha, 5.1% beta 15 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... 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 314 through 325 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 359 through 370 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 461 through 466 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.914A pdb=" N ILE A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASP A 504 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 508 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 509 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.996A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 542 removed outlier: 4.432A pdb=" N ASN A 537 " --> pdb=" O HIS A 533 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 566 through 571 removed outlier: 4.079A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 4.092A 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 595 removed outlier: 3.650A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 7.203A 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 removed outlier: 3.899A pdb=" N ILE A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 Proline residue: A 642 - end of helix removed outlier: 4.060A pdb=" N LEU A 647 " --> pdb=" O HIS A 644 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 648 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 669 through 689 removed outlier: 3.880A pdb=" N ILE A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 86 through 97 removed outlier: 4.642A pdb=" N ASN B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 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 214 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 275 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 removed outlier: 3.620A pdb=" N GLU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.954A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.767A 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: 3.952A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) 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 258 through 269 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 293 through 312 Processing helix chain 'C' and resid 316 through 334 removed outlier: 3.895A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.758A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 91 Proline residue: D 85 - end of helix removed outlier: 4.166A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.844A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (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 152 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 198 through 207 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 277 Processing helix chain 'D' and resid 280 through 291 Processing helix chain 'D' and resid 297 through 308 Processing helix chain 'D' and resid 316 through 334 Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 21 through 32 removed outlier: 4.052A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 105 through 118 removed outlier: 4.353A pdb=" N GLN E 118 " --> pdb=" O LYS E 114 " (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: 3.830A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 216 through 226 removed outlier: 3.514A pdb=" N LEU E 219 " --> pdb=" O LYS E 216 " (cutoff:3.500A) 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 291 Processing helix chain 'E' and resid 296 through 309 Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 338 through 353 removed outlier: 3.545A pdb=" N LEU E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 349 through 351 removed outlier: 8.715A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP A 424 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 45 through 48 removed outlier: 4.070A pdb=" N MET B 45 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 76 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.615A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 6.009A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 189 removed outlier: 6.314A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4707 1.36 - 1.51: 3925 1.51 - 1.66: 5953 1.66 - 1.80: 61 1.80 - 1.95: 44 Bond restraints: 14690 Sorted by residual: bond pdb=" N ILE A 547 " pdb=" CA ILE A 547 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N ASN A 546 " pdb=" CA ASN A 546 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.53e+00 bond pdb=" N LEU A 549 " pdb=" CA LEU A 549 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.36e+00 bond pdb=" N GLU A 544 " pdb=" CA GLU A 544 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.25e-02 6.40e+03 5.80e+00 bond pdb=" N LYS A 550 " pdb=" CA LYS A 550 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.60e-02 3.91e+03 5.28e+00 ... (remaining 14685 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.50: 644 106.50 - 113.95: 8590 113.95 - 121.40: 7388 121.40 - 128.86: 3327 128.86 - 136.31: 119 Bond angle restraints: 20068 Sorted by residual: angle pdb=" N VAL B 88 " pdb=" CA VAL B 88 " pdb=" C VAL B 88 " ideal model delta sigma weight residual 111.62 106.86 4.76 7.90e-01 1.60e+00 3.63e+01 angle pdb=" CA PRO A 500 " pdb=" N PRO A 500 " pdb=" CD PRO A 500 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.76e+01 angle pdb=" N GLU C 332 " pdb=" CA GLU C 332 " pdb=" C GLU C 332 " ideal model delta sigma weight residual 112.54 107.29 5.25 1.22e+00 6.72e-01 1.85e+01 angle pdb=" C LEU B 300 " pdb=" N GLU B 301 " pdb=" CA GLU B 301 " ideal model delta sigma weight residual 120.72 114.15 6.57 1.67e+00 3.59e-01 1.55e+01 angle pdb=" CA GLU C 118 " pdb=" CB GLU C 118 " pdb=" CG GLU C 118 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 ... (remaining 20063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.06: 8362 29.06 - 58.12: 432 58.12 - 87.18: 29 87.18 - 116.24: 3 116.24 - 145.30: 1 Dihedral angle restraints: 8827 sinusoidal: 3910 harmonic: 4917 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 -169.47 109.47 1 2.00e+01 2.50e-03 3.20e+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 77.57 -145.30 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" CA LEU B 67 " pdb=" C LEU B 67 " pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 8824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1603 0.035 - 0.071: 512 0.071 - 0.106: 155 0.106 - 0.142: 46 0.142 - 0.177: 9 Chirality restraints: 2325 Sorted by residual: chirality pdb=" CA ILE A 547 " pdb=" N ILE A 547 " pdb=" C ILE A 547 " pdb=" CB ILE A 547 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA GLU E 58 " pdb=" N GLU E 58 " pdb=" C GLU E 58 " pdb=" CB GLU E 58 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA GLU C 118 " pdb=" N GLU C 118 " pdb=" C GLU C 118 " pdb=" CB GLU C 118 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 2322 not shown) Planarity restraints: 2379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " -0.099 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO A 500 " 0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 54 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C MET E 54 " 0.034 2.00e-02 2.50e+03 pdb=" O MET E 54 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA E 55 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 605 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 606 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.024 5.00e-02 4.00e+02 ... (remaining 2376 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 264 2.65 - 3.22: 13658 3.22 - 3.78: 24089 3.78 - 4.34: 32260 4.34 - 4.90: 51219 Nonbonded interactions: 121490 Sorted by model distance: nonbonded pdb=" O1B AGS B 401 " pdb="MG MG B 402 " model vdw 2.092 2.170 nonbonded pdb=" OD2 ASP A 424 " pdb="MG MG A 902 " model vdw 2.097 2.170 nonbonded pdb=" O3G AGS A 901 " pdb="MG MG A 902 " model vdw 2.102 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.123 2.170 nonbonded pdb=" O1A AGS B 401 " pdb="MG MG B 402 " model vdw 2.126 2.170 ... (remaining 121485 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 14.440 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.750 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 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 0.093 14690 Z= 0.193 Angle : 0.647 8.431 20068 Z= 0.364 Chirality : 0.040 0.177 2325 Planarity : 0.005 0.146 2379 Dihedral : 15.672 145.303 5629 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.13 % 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: 0.18 (0.21), residues: 1664 helix: 0.68 (0.17), residues: 974 sheet: -0.31 (0.46), residues: 140 loop : -0.61 (0.26), residues: 550 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 1.812 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 241 average time/residue: 0.2479 time to fit residues: 91.4274 Evaluate side-chains 190 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1363 time to fit residues: 2.4548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 133 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 319 GLN ** C 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN E 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 14690 Z= 0.298 Angle : 0.637 8.888 20068 Z= 0.331 Chirality : 0.042 0.154 2325 Planarity : 0.005 0.081 2379 Dihedral : 15.659 161.867 2299 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 2.22 % 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: 0.05 (0.21), residues: 1664 helix: 0.65 (0.17), residues: 968 sheet: -0.48 (0.43), residues: 153 loop : -0.77 (0.27), residues: 543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 213 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 29 residues processed: 226 average time/residue: 0.2561 time to fit residues: 87.8850 Evaluate side-chains 219 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1389 time to fit residues: 9.8235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS B 177 GLN B 204 GLN B 208 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 227 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14690 Z= 0.210 Angle : 0.563 9.422 20068 Z= 0.293 Chirality : 0.039 0.185 2325 Planarity : 0.004 0.066 2379 Dihedral : 15.557 158.694 2299 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.74 % 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: 0.21 (0.21), residues: 1664 helix: 0.79 (0.17), residues: 966 sheet: -0.41 (0.43), residues: 153 loop : -0.71 (0.27), residues: 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 215 average time/residue: 0.2574 time to fit residues: 83.9060 Evaluate side-chains 194 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2043 time to fit residues: 4.6906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 81 optimal weight: 0.0770 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 329 ASN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 14690 Z= 0.176 Angle : 0.546 9.925 20068 Z= 0.283 Chirality : 0.038 0.160 2325 Planarity : 0.004 0.058 2379 Dihedral : 15.464 157.405 2299 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.14 % 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: 0.32 (0.21), residues: 1664 helix: 0.91 (0.17), residues: 963 sheet: -0.46 (0.43), residues: 151 loop : -0.70 (0.27), residues: 550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 208 average time/residue: 0.2860 time to fit residues: 89.5813 Evaluate side-chains 195 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1631 time to fit residues: 5.1967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 14690 Z= 0.247 Angle : 0.595 9.777 20068 Z= 0.308 Chirality : 0.041 0.212 2325 Planarity : 0.004 0.052 2379 Dihedral : 15.586 166.321 2299 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 1.82 % 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: 0.13 (0.21), residues: 1664 helix: 0.78 (0.17), residues: 963 sheet: -0.66 (0.42), residues: 159 loop : -0.79 (0.27), residues: 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.690 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 211 average time/residue: 0.2579 time to fit residues: 83.7302 Evaluate side-chains 194 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1612 time to fit residues: 6.7014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 0.0050 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 0.0000 chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN B 34 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 319 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 14690 Z= 0.175 Angle : 0.561 9.986 20068 Z= 0.292 Chirality : 0.039 0.194 2325 Planarity : 0.004 0.049 2379 Dihedral : 15.466 160.187 2299 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.08 % 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: 0.34 (0.21), residues: 1664 helix: 0.96 (0.17), residues: 962 sheet: -0.63 (0.43), residues: 157 loop : -0.68 (0.27), residues: 545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 1.752 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 203 average time/residue: 0.2553 time to fit residues: 78.9924 Evaluate side-chains 187 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 1.681 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1362 time to fit residues: 4.5092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN C 319 GLN E 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 14690 Z= 0.372 Angle : 0.692 9.776 20068 Z= 0.355 Chirality : 0.044 0.216 2325 Planarity : 0.005 0.047 2379 Dihedral : 15.783 176.754 2299 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 1.68 % 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 (0.20), residues: 1664 helix: 0.42 (0.16), residues: 976 sheet: -0.81 (0.42), residues: 159 loop : -1.00 (0.27), residues: 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 199 average time/residue: 0.2448 time to fit residues: 75.7247 Evaluate side-chains 186 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 1.683 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1321 time to fit residues: 5.4219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN C 319 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14690 Z= 0.214 Angle : 0.601 10.999 20068 Z= 0.311 Chirality : 0.040 0.183 2325 Planarity : 0.004 0.047 2379 Dihedral : 15.650 172.623 2299 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 1.01 % 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: 0.02 (0.21), residues: 1664 helix: 0.71 (0.17), residues: 967 sheet: -0.79 (0.42), residues: 157 loop : -0.86 (0.27), residues: 540 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 1.738 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 200 average time/residue: 0.2583 time to fit residues: 79.5813 Evaluate side-chains 191 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 181 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1374 time to fit residues: 4.8574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 chunk 100 optimal weight: 0.3980 chunk 161 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN C 319 GLN D 24 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 14690 Z= 0.189 Angle : 0.592 10.378 20068 Z= 0.307 Chirality : 0.040 0.201 2325 Planarity : 0.004 0.046 2379 Dihedral : 15.549 169.626 2299 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.34 % 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: 0.21 (0.21), residues: 1664 helix: 0.87 (0.17), residues: 967 sheet: -0.79 (0.43), residues: 157 loop : -0.76 (0.28), residues: 540 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 192 time to evaluate : 1.638 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 194 average time/residue: 0.2458 time to fit residues: 73.9650 Evaluate side-chains 183 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1429 time to fit residues: 2.6725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 112 optimal weight: 0.1980 chunk 169 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 107 optimal weight: 0.4980 chunk 143 optimal weight: 6.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 146 GLN B 148 ASN C 319 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14690 Z= 0.176 Angle : 0.598 11.424 20068 Z= 0.310 Chirality : 0.039 0.168 2325 Planarity : 0.004 0.046 2379 Dihedral : 15.459 165.329 2299 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.61 % 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: 0.33 (0.21), residues: 1664 helix: 0.96 (0.17), residues: 967 sheet: -0.78 (0.43), residues: 157 loop : -0.69 (0.28), residues: 540 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 1.683 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 187 average time/residue: 0.2462 time to fit residues: 71.0556 Evaluate side-chains 183 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1416 time to fit residues: 3.4846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 0.0470 chunk 7 optimal weight: 0.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 146 GLN B 148 ASN C 319 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.186473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.158439 restraints weight = 20598.464| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.24 r_work: 0.4091 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14690 Z= 0.206 Angle : 0.612 11.399 20068 Z= 0.316 Chirality : 0.040 0.173 2325 Planarity : 0.004 0.045 2379 Dihedral : 15.481 166.613 2299 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.34 % 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: 0.30 (0.21), residues: 1664 helix: 0.92 (0.17), residues: 968 sheet: -0.81 (0.43), residues: 159 loop : -0.66 (0.28), residues: 537 =============================================================================== Job complete usr+sys time: 3059.81 seconds wall clock time: 56 minutes 46.35 seconds (3406.35 seconds total)