Starting phenix.real_space_refine on Fri Feb 16 06:23:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/02_2024/7tfk_25875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/02_2024/7tfk_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_25875/02_2024/7tfk_25875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/02_2024/7tfk_25875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/02_2024/7tfk_25875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfk_25875/02_2024/7tfk_25875_updated.pdb" } resolution = 3.25 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= -0.001 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.61, per 1000 atoms: 0.60 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: 7.05 Conformation dependent library (CDL) restraints added in 2.8 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: 6.39 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: 4.30 Time building geometry restraints manager: 7.09 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: 8420 29.06 - 58.12: 466 58.12 - 87.18: 29 87.18 - 116.24: 3 116.24 - 145.30: 1 Dihedral angle restraints: 8919 sinusoidal: 4002 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 8916 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 15.100 Check model and map are aligned: 0.180 Set scattering table: 0.140 Process input model: 45.580 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.910 ------------------------------------------------------------------------------- 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 : 16.009 145.303 5721 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 % Allowed : 0.40 % Favored : 99.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 259 HIS 0.009 0.001 HIS C 260 PHE 0.016 0.001 PHE D 280 TYR 0.022 0.002 TYR C 71 ARG 0.005 0.000 ARG A 632 *********************** 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 : 1.612 Fit side-chains REVERT: A 423 MET cc_start: 0.6285 (ppp) cc_final: 0.5788 (ppp) REVERT: B 50 MET cc_start: 0.4995 (pmm) cc_final: 0.4573 (pmm) REVERT: B 177 GLN cc_start: 0.6174 (mt0) cc_final: 0.5295 (mm-40) REVERT: C 135 GLU cc_start: 0.5772 (mm-30) cc_final: 0.5347 (mm-30) REVERT: C 200 LEU cc_start: 0.5980 (tt) cc_final: 0.5088 (pp) outliers start: 2 outliers final: 1 residues processed: 241 average time/residue: 0.2356 time to fit residues: 86.5876 Evaluate side-chains 191 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ASN 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: 0.9990 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: 1.1384 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14690 Z= 0.263 Angle : 0.603 8.840 20068 Z= 0.315 Chirality : 0.041 0.148 2325 Planarity : 0.004 0.080 2379 Dihedral : 16.049 159.115 2393 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.02 % Allowed : 7.95 % Favored : 90.03 % 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: 0.74 (0.17), residues: 974 sheet: -0.58 (0.44), residues: 148 loop : -0.74 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 669 HIS 0.008 0.001 HIS B 44 PHE 0.017 0.002 PHE A 443 TYR 0.017 0.002 TYR B 186 ARG 0.006 0.001 ARG B 253 *********************** 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 238 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5565 (tmm) cc_final: 0.4966 (mmp) REVERT: A 628 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7347 (tm-30) REVERT: B 50 MET cc_start: 0.4838 (pmm) cc_final: 0.4019 (pmm) REVERT: B 177 GLN cc_start: 0.6187 (mt0) cc_final: 0.5424 (mm110) REVERT: C 135 GLU cc_start: 0.6218 (mm-30) cc_final: 0.5765 (mm-30) REVERT: C 148 ASN cc_start: 0.6815 (m110) cc_final: 0.6506 (m-40) REVERT: C 200 LEU cc_start: 0.6008 (tt) cc_final: 0.5163 (pp) outliers start: 30 outliers final: 26 residues processed: 219 average time/residue: 0.2567 time to fit residues: 83.9301 Evaluate side-chains 219 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 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** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 227 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.1649 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= 0.196 Angle : 0.550 9.307 20068 Z= 0.287 Chirality : 0.039 0.173 2325 Planarity : 0.004 0.065 2379 Dihedral : 15.924 159.816 2391 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.75 % Allowed : 11.52 % Favored : 86.73 % 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: 0.28 (0.21), residues: 1664 helix: 0.81 (0.17), residues: 973 sheet: -0.36 (0.44), residues: 147 loop : -0.64 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 669 HIS 0.004 0.001 HIS B 44 PHE 0.013 0.002 PHE A 496 TYR 0.018 0.002 TYR B 186 ARG 0.005 0.000 ARG B 253 *********************** 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 236 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5506 (tmm) cc_final: 0.4994 (mmp) REVERT: B 177 GLN cc_start: 0.6123 (mt0) cc_final: 0.5367 (mm110) REVERT: C 135 GLU cc_start: 0.6028 (mm-30) cc_final: 0.5641 (mm-30) REVERT: C 200 LEU cc_start: 0.5896 (tt) cc_final: 0.5135 (pp) REVERT: C 334 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6911 (pt0) REVERT: E 66 TYR cc_start: 0.5391 (m-80) cc_final: 0.4902 (m-80) outliers start: 26 outliers final: 20 residues processed: 221 average time/residue: 0.2493 time to fit residues: 83.0236 Evaluate side-chains 212 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 155 optimal weight: 0.2980 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** D 338 ASN E 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14690 Z= 0.204 Angle : 0.559 9.704 20068 Z= 0.291 Chirality : 0.039 0.173 2325 Planarity : 0.004 0.057 2379 Dihedral : 15.877 162.833 2391 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.69 % Allowed : 13.74 % Favored : 83.57 % 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: 0.28 (0.21), residues: 1664 helix: 0.84 (0.17), residues: 973 sheet: -0.46 (0.43), residues: 151 loop : -0.65 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 669 HIS 0.004 0.001 HIS B 232 PHE 0.017 0.002 PHE A 443 TYR 0.021 0.002 TYR C 71 ARG 0.007 0.000 ARG B 253 *********************** 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 248 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5585 (tmm) cc_final: 0.4969 (mmp) REVERT: A 628 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 177 GLN cc_start: 0.6141 (mt0) cc_final: 0.5391 (mm110) REVERT: C 199 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: C 334 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6950 (pt0) REVERT: E 66 TYR cc_start: 0.5294 (m-80) cc_final: 0.4785 (m-80) outliers start: 40 outliers final: 29 residues processed: 227 average time/residue: 0.2467 time to fit residues: 84.3569 Evaluate side-chains 218 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 312 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN C 12 ASN C 319 GLN E 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14690 Z= 0.333 Angle : 0.666 9.450 20068 Z= 0.345 Chirality : 0.043 0.219 2325 Planarity : 0.005 0.052 2379 Dihedral : 16.130 174.853 2391 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.84 % Allowed : 14.61 % Favored : 81.55 % 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 (0.20), residues: 1664 helix: 0.37 (0.16), residues: 979 sheet: -0.71 (0.42), residues: 154 loop : -0.96 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 669 HIS 0.006 0.001 HIS A 644 PHE 0.019 0.002 PHE A 496 TYR 0.022 0.002 TYR D 31 ARG 0.008 0.001 ARG C 206 *********************** 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 259 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.5549 (tmm) cc_final: 0.5168 (mmp) REVERT: A 538 GLU cc_start: 0.7044 (mp0) cc_final: 0.6829 (mp0) REVERT: B 256 LEU cc_start: 0.7292 (mp) cc_final: 0.6981 (mp) REVERT: C 200 LEU cc_start: 0.6232 (tt) cc_final: 0.5249 (pp) REVERT: C 334 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7191 (pt0) REVERT: E 7 LYS cc_start: 0.8044 (pttt) cc_final: 0.7181 (ptpp) REVERT: E 58 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6848 (mm-30) outliers start: 57 outliers final: 38 residues processed: 234 average time/residue: 0.2401 time to fit residues: 86.2292 Evaluate side-chains 218 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN C 12 ASN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14690 Z= 0.182 Angle : 0.567 9.847 20068 Z= 0.295 Chirality : 0.039 0.162 2325 Planarity : 0.004 0.050 2379 Dihedral : 15.847 165.326 2391 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.56 % Allowed : 16.57 % Favored : 80.88 % 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: 0.10 (0.21), residues: 1664 helix: 0.72 (0.17), residues: 974 sheet: -0.66 (0.43), residues: 152 loop : -0.75 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 669 HIS 0.006 0.001 HIS B 44 PHE 0.016 0.002 PHE A 443 TYR 0.017 0.001 TYR B 186 ARG 0.005 0.000 ARG B 90 *********************** 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 233 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.5521 (ppp) REVERT: A 429 MET cc_start: 0.5621 (tmm) cc_final: 0.5233 (mmp) REVERT: A 538 GLU cc_start: 0.6930 (mp0) cc_final: 0.6570 (mp0) REVERT: B 26 ASN cc_start: 0.5837 (OUTLIER) cc_final: 0.5591 (p0) REVERT: B 256 LEU cc_start: 0.7252 (mp) cc_final: 0.6874 (mt) REVERT: C 174 ILE cc_start: 0.4915 (OUTLIER) cc_final: 0.4662 (mm) REVERT: C 200 LEU cc_start: 0.6054 (tt) cc_final: 0.5104 (pp) REVERT: C 334 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: E 20 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6803 (mm-30) outliers start: 38 outliers final: 23 residues processed: 214 average time/residue: 0.2423 time to fit residues: 79.1112 Evaluate side-chains 210 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.6530 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14690 Z= 0.241 Angle : 0.593 9.701 20068 Z= 0.306 Chirality : 0.040 0.180 2325 Planarity : 0.004 0.047 2379 Dihedral : 15.876 168.023 2391 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.76 % Allowed : 17.24 % Favored : 80.00 % 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: 0.06 (0.21), residues: 1664 helix: 0.70 (0.17), residues: 974 sheet: -0.73 (0.43), residues: 154 loop : -0.77 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 669 HIS 0.004 0.001 HIS B 232 PHE 0.015 0.002 PHE A 443 TYR 0.018 0.002 TYR C 75 ARG 0.006 0.000 ARG C 206 *********************** 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 236 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: A 423 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5447 (ppp) REVERT: A 614 VAL cc_start: 0.7053 (OUTLIER) cc_final: 0.6810 (t) REVERT: C 174 ILE cc_start: 0.5122 (OUTLIER) cc_final: 0.4875 (mm) REVERT: C 334 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7139 (pt0) REVERT: E 174 MET cc_start: 0.3761 (mtm) cc_final: 0.3156 (mtm) REVERT: E 328 PHE cc_start: 0.6926 (m-80) cc_final: 0.6490 (m-80) outliers start: 41 outliers final: 29 residues processed: 214 average time/residue: 0.2438 time to fit residues: 80.0803 Evaluate side-chains 218 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 149 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 26 ASN B 34 GLN C 319 GLN D 334 ASN E 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14690 Z= 0.186 Angle : 0.573 11.050 20068 Z= 0.297 Chirality : 0.039 0.201 2325 Planarity : 0.004 0.047 2379 Dihedral : 15.734 162.301 2391 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.42 % Allowed : 18.32 % Favored : 79.26 % 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: 0.22 (0.21), residues: 1664 helix: 0.82 (0.17), residues: 977 sheet: -0.78 (0.43), residues: 154 loop : -0.66 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 669 HIS 0.005 0.001 HIS B 44 PHE 0.014 0.001 PHE A 443 TYR 0.018 0.001 TYR B 186 ARG 0.005 0.000 ARG C 206 *********************** 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 226 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 1.600 Fit side-chains REVERT: A 423 MET cc_start: 0.5808 (ppp) cc_final: 0.5489 (ppp) REVERT: B 110 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7322 (mp) REVERT: B 256 LEU cc_start: 0.7271 (mp) cc_final: 0.6979 (mp) REVERT: C 174 ILE cc_start: 0.5061 (mm) cc_final: 0.4815 (mm) REVERT: C 200 LEU cc_start: 0.6265 (tt) cc_final: 0.5257 (pp) REVERT: C 334 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7068 (pt0) REVERT: D 24 GLN cc_start: 0.5432 (mp-120) cc_final: 0.5153 (mp10) REVERT: E 7 LYS cc_start: 0.8101 (pttt) cc_final: 0.7353 (ptpp) REVERT: E 25 PHE cc_start: 0.5271 (t80) cc_final: 0.4985 (t80) REVERT: E 174 MET cc_start: 0.3683 (mtm) cc_final: 0.3002 (mtm) outliers start: 36 outliers final: 29 residues processed: 208 average time/residue: 0.2276 time to fit residues: 73.0809 Evaluate side-chains 216 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 100 optimal weight: 0.0370 chunk 161 optimal weight: 0.8980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 26 ASN B 34 GLN C 319 GLN D 334 ASN E 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14690 Z= 0.202 Angle : 0.586 10.719 20068 Z= 0.301 Chirality : 0.040 0.214 2325 Planarity : 0.004 0.046 2379 Dihedral : 15.742 163.758 2391 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.90 % Allowed : 18.32 % Favored : 78.79 % 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: 0.19 (0.21), residues: 1664 helix: 0.81 (0.17), residues: 980 sheet: -0.79 (0.43), residues: 154 loop : -0.71 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 669 HIS 0.004 0.001 HIS B 44 PHE 0.014 0.002 PHE A 443 TYR 0.017 0.001 TYR B 186 ARG 0.006 0.000 ARG C 206 *********************** 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 236 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 1.608 Fit side-chains REVERT: A 423 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.5395 (ppp) REVERT: A 614 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6774 (t) REVERT: B 256 LEU cc_start: 0.7239 (mp) cc_final: 0.6929 (mp) REVERT: C 174 ILE cc_start: 0.5044 (OUTLIER) cc_final: 0.4843 (mm) REVERT: C 200 LEU cc_start: 0.6185 (tt) cc_final: 0.5253 (pp) REVERT: C 334 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7050 (pt0) REVERT: D 24 GLN cc_start: 0.5371 (mp-120) cc_final: 0.5114 (mp10) REVERT: E 7 LYS cc_start: 0.8128 (pttt) cc_final: 0.7393 (ptpp) REVERT: E 25 PHE cc_start: 0.5372 (t80) cc_final: 0.5136 (t80) outliers start: 43 outliers final: 35 residues processed: 216 average time/residue: 0.2691 time to fit residues: 90.0988 Evaluate side-chains 225 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 186 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 349 VAL 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: 0.9980 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.0870 chunk 107 optimal weight: 0.1980 chunk 143 optimal weight: 5.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 26 ASN ** 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: 0.6508 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14690 Z= 0.225 Angle : 0.612 10.580 20068 Z= 0.315 Chirality : 0.040 0.193 2325 Planarity : 0.004 0.046 2379 Dihedral : 15.753 164.908 2391 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.10 % Allowed : 18.32 % Favored : 78.59 % 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: 0.21 (0.21), residues: 1664 helix: 0.84 (0.17), residues: 974 sheet: -0.77 (0.43), residues: 154 loop : -0.71 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 669 HIS 0.004 0.001 HIS B 44 PHE 0.014 0.002 PHE A 443 TYR 0.017 0.002 TYR C 75 ARG 0.006 0.000 ARG C 206 ********************** 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 234 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 1.691 Fit side-chains REVERT: A 423 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5391 (ppp) REVERT: A 614 VAL cc_start: 0.7082 (OUTLIER) cc_final: 0.6813 (t) REVERT: B 90 ARG cc_start: 0.5658 (ptt90) cc_final: 0.5213 (pmt170) REVERT: B 110 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7262 (mp) REVERT: B 256 LEU cc_start: 0.7191 (mp) cc_final: 0.6873 (mp) REVERT: C 174 ILE cc_start: 0.5072 (OUTLIER) cc_final: 0.4863 (mm) REVERT: C 200 LEU cc_start: 0.6163 (tt) cc_final: 0.5259 (pp) REVERT: C 334 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7068 (pt0) REVERT: D 24 GLN cc_start: 0.5484 (mp-120) cc_final: 0.5241 (mp10) REVERT: E 7 LYS cc_start: 0.8136 (pttt) cc_final: 0.7395 (ptpp) REVERT: E 25 PHE cc_start: 0.5335 (t80) cc_final: 0.5083 (t80) REVERT: E 70 ILE cc_start: 0.6733 (tp) cc_final: 0.6426 (tp) REVERT: E 328 PHE cc_start: 0.6853 (m-80) cc_final: 0.6427 (m-80) outliers start: 46 outliers final: 35 residues processed: 213 average time/residue: 0.2420 time to fit residues: 79.8011 Evaluate side-chains 224 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 184 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 146 GLN B 148 ASN C 319 GLN D 334 ASN E 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.184639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.157422 restraints weight = 20674.814| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.30 r_work: 0.4084 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14690 Z= 0.183 Angle : 0.579 10.383 20068 Z= 0.299 Chirality : 0.039 0.188 2325 Planarity : 0.004 0.046 2379 Dihedral : 15.644 160.741 2391 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.56 % Allowed : 18.45 % Favored : 78.99 % 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: 0.94 (0.17), residues: 975 sheet: -0.78 (0.44), residues: 154 loop : -0.63 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 669 HIS 0.005 0.001 HIS B 44 PHE 0.014 0.001 PHE A 443 TYR 0.017 0.001 TYR B 186 ARG 0.006 0.000 ARG C 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3139.00 seconds wall clock time: 58 minutes 51.62 seconds (3531.62 seconds total)