Starting phenix.real_space_refine on Thu Jun 12 10:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlh_22244/06_2025/6xlh_22244.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlh_22244/06_2025/6xlh_22244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xlh_22244/06_2025/6xlh_22244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlh_22244/06_2025/6xlh_22244.map" model { file = "/net/cci-nas-00/data/ceres_data/6xlh_22244/06_2025/6xlh_22244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlh_22244/06_2025/6xlh_22244.cif" } resolution = 2.83 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 5 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 8696 2.51 5 N 2240 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13608 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "C" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2544 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.91, per 1000 atoms: 0.65 Number of scatterers: 13608 At special positions: 0 Unit cell: (104.394, 113.436, 132.342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 26 16.00 P 5 15.00 Mg 2 11.99 O 2637 8.00 N 2240 7.00 C 8696 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 40.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 4.457A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 50 removed outlier: 4.083A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 85 through 92 removed outlier: 3.695A pdb=" N ILE A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.642A pdb=" N SER A 126 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.825A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 197 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.578A pdb=" N TYR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.569A pdb=" N PHE A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.678A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.590A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 459 Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.566A pdb=" N VAL A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 removed outlier: 4.372A pdb=" N LEU A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 510 removed outlier: 4.456A pdb=" N TYR A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 510 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 615 through 627 Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.523A pdb=" N LEU A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.965A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.787A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 50 removed outlier: 4.143A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.659A pdb=" N GLU B 57 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.717A pdb=" N ILE B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.780A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.528A pdb=" N SER B 126 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.755A pdb=" N TYR B 184 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 195 removed outlier: 3.763A pdb=" N ILE B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.628A pdb=" N TYR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 406 removed outlier: 3.908A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.603A pdb=" N ASP B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.622A pdb=" N VAL B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.652A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 459 Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.509A pdb=" N VAL B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 removed outlier: 4.427A pdb=" N LEU B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.952A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 510 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 543 Processing helix chain 'B' and resid 543 through 555 Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.580A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 627 Processing helix chain 'B' and resid 632 through 651 removed outlier: 3.664A pdb=" N LEU B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.789A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.675A pdb=" N TRP C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.569A pdb=" N SER C 121 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.510A pdb=" N ILE C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 150 removed outlier: 3.827A pdb=" N GLY C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.619A pdb=" N ASN C 169 " --> pdb=" O TYR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.682A pdb=" N GLU C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 removed outlier: 3.855A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.666A pdb=" N GLU C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 removed outlier: 3.765A pdb=" N ILE C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.731A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 removed outlier: 3.955A pdb=" N ALA D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.682A pdb=" N ILE D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.523A pdb=" N GLU A 4 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.599A pdb=" N GLN A 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 265 removed outlier: 6.102A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.727A pdb=" N ALA A 315 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 307 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 339 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 452 removed outlier: 4.033A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 560 through 563 removed outlier: 6.431A pdb=" N LYS A 560 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 611 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 562 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307 removed outlier: 7.286A pdb=" N LEU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.890A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.550A pdb=" N LYS B 560 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 611 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 562 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.616A pdb=" N VAL C 12 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN C 58 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 32 through 34 removed outlier: 8.176A pdb=" N LYS C 43 " --> pdb=" O HIS C 78 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N HIS C 78 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS C 45 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLU C 76 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL C 47 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 74 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 77 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 213 through 218 removed outlier: 6.854A pdb=" N ILE C 216 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR C 318 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU C 218 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS C 316 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.706A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 213 through 218 removed outlier: 6.937A pdb=" N ILE D 216 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR D 318 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU D 218 " --> pdb=" O LYS D 316 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS D 316 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 274 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS D 284 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU D 272 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS D 286 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER D 270 " --> pdb=" O LYS D 286 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 259 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 222 596 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.44 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 4495 1.37 - 1.52: 4085 1.52 - 1.66: 5235 1.66 - 1.81: 42 1.81 - 1.95: 5 Bond restraints: 13862 Sorted by residual: bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.472 0.018 2.00e-02 2.50e+03 8.34e-01 bond pdb=" C ALA C 292 " pdb=" N PRO C 293 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.66e-01 bond pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 1.245 1.235 0.010 1.41e-02 5.03e+03 5.11e-01 bond pdb=" C GLU B 655 " pdb=" N GLU B 656 " ideal model delta sigma weight residual 1.331 1.343 -0.012 2.07e-02 2.33e+03 3.60e-01 bond pdb=" N ILE C 320 " pdb=" CA ILE C 320 " ideal model delta sigma weight residual 1.461 1.468 -0.007 1.23e-02 6.61e+03 2.86e-01 ... (remaining 13857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 18451 1.36 - 2.72: 187 2.72 - 4.08: 48 4.08 - 5.43: 17 5.43 - 6.79: 1 Bond angle restraints: 18704 Sorted by residual: angle pdb=" N VAL A 23 " pdb=" CA VAL A 23 " pdb=" C VAL A 23 " ideal model delta sigma weight residual 113.71 108.38 5.33 9.50e-01 1.11e+00 3.15e+01 angle pdb=" N ILE B 384 " pdb=" CA ILE B 384 " pdb=" C ILE B 384 " ideal model delta sigma weight residual 113.53 108.18 5.35 9.80e-01 1.04e+00 2.98e+01 angle pdb=" N ILE A 384 " pdb=" CA ILE A 384 " pdb=" C ILE A 384 " ideal model delta sigma weight residual 113.53 108.69 4.84 9.80e-01 1.04e+00 2.44e+01 angle pdb=" CA ILE B 384 " pdb=" C ILE B 384 " pdb=" N MET B 385 " ideal model delta sigma weight residual 119.31 116.30 3.01 1.15e+00 7.56e-01 6.83e+00 angle pdb=" CA ILE A 384 " pdb=" C ILE A 384 " pdb=" N MET A 385 " ideal model delta sigma weight residual 119.31 116.51 2.80 1.15e+00 7.56e-01 5.94e+00 ... (remaining 18699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.51: 8413 33.51 - 67.01: 30 67.01 - 100.52: 0 100.52 - 134.03: 2 134.03 - 167.53: 1 Dihedral angle restraints: 8446 sinusoidal: 3542 harmonic: 4904 Sorted by residual: dihedral pdb=" O2A ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PA ADP B 801 " pdb=" PB ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 132.47 167.53 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B AGS A 801 " pdb=" O3B AGS A 801 " pdb=" PB AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sinusoidal sigma weight residual 68.91 -44.98 113.89 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" O1A AGS A 801 " pdb=" O3A AGS A 801 " pdb=" PA AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sinusoidal sigma weight residual -67.73 -173.26 105.53 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 8443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1362 0.030 - 0.059: 500 0.059 - 0.089: 102 0.089 - 0.118: 106 0.118 - 0.148: 17 Chirality restraints: 2087 Sorted by residual: chirality pdb=" CA ILE C 154 " pdb=" N ILE C 154 " pdb=" C ILE C 154 " pdb=" CB ILE C 154 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE C 320 " pdb=" N ILE C 320 " pdb=" C ILE C 320 " pdb=" CB ILE C 320 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA VAL C 95 " pdb=" N VAL C 95 " pdb=" C VAL C 95 " pdb=" CB VAL C 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 2084 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 355 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 320 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO C 321 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 354 " 0.016 5.00e-02 4.00e+02 2.50e-02 9.99e-01 pdb=" N PRO B 355 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " 0.014 5.00e-02 4.00e+02 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 320 2.70 - 3.31: 14840 3.31 - 3.92: 26511 3.92 - 4.53: 35564 4.53 - 5.14: 56834 Nonbonded interactions: 134069 Sorted by model distance: nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.093 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.134 2.170 nonbonded pdb=" OH TYR A 301 " pdb=" OE1 GLU A 402 " model vdw 2.253 3.040 nonbonded pdb=" O LYS A 480 " pdb=" OG1 THR B 658 " model vdw 2.256 3.040 ... (remaining 134064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 675 or resid 802 through 803)) selection = (chain 'B' and (resid 3 through 675 or resid 802 through 803)) } 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 34.480 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.001 0.020 13862 Z= 0.067 Angle : 0.388 6.793 18704 Z= 0.223 Chirality : 0.039 0.148 2087 Planarity : 0.002 0.032 2388 Dihedral : 7.607 167.535 5254 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.13 % Allowed : 2.73 % Favored : 97.13 % 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: -3.84 (0.16), residues: 1653 helix: -3.18 (0.12), residues: 613 sheet: -1.62 (0.25), residues: 362 loop : -2.23 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 273 HIS 0.001 0.000 HIS B 304 PHE 0.004 0.000 PHE A 609 TYR 0.008 0.000 TYR A 24 ARG 0.001 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.26959 ( 582) hydrogen bonds : angle 8.36180 ( 1650) covalent geometry : bond 0.00118 (13862) covalent geometry : angle 0.38769 (18704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 474 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7516 (mtpp) REVERT: C 301 THR cc_start: 0.8435 (m) cc_final: 0.8193 (m) REVERT: C 325 GLU cc_start: 0.7229 (pt0) cc_final: 0.6989 (pm20) outliers start: 2 outliers final: 0 residues processed: 475 average time/residue: 1.5598 time to fit residues: 795.9397 Evaluate side-chains 193 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 135 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 380 GLN A 381 GLN A 409 GLN A 463 HIS B 14 GLN B 26 ASN B 55 GLN B 91 ASN B 335 ASN B 463 HIS C 4 ASN C 57 ASN C 94 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 267 ASN C 306 GLN D 207 GLN D 303 HIS D 314 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107794 restraints weight = 21726.624| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.79 r_work: 0.3292 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 13862 Z= 0.260 Angle : 0.671 7.262 18704 Z= 0.353 Chirality : 0.048 0.199 2087 Planarity : 0.005 0.043 2388 Dihedral : 7.061 152.475 1813 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.53 % Allowed : 14.47 % Favored : 81.00 % 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: -1.96 (0.19), residues: 1653 helix: -0.82 (0.18), residues: 624 sheet: -1.39 (0.25), residues: 382 loop : -1.50 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 285 HIS 0.008 0.002 HIS A 463 PHE 0.018 0.002 PHE C 264 TYR 0.013 0.002 TYR C 23 ARG 0.010 0.001 ARG B 575 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 582) hydrogen bonds : angle 5.49920 ( 1650) covalent geometry : bond 0.00606 (13862) covalent geometry : angle 0.67129 (18704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 165 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: A 211 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7830 (mmtm) REVERT: A 339 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8984 (tt) REVERT: A 368 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: A 381 GLN cc_start: 0.6917 (pt0) cc_final: 0.6709 (pt0) REVERT: A 559 GLU cc_start: 0.7678 (tt0) cc_final: 0.6812 (mt-10) REVERT: A 623 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7432 (mptt) REVERT: B 149 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: B 377 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: B 427 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: B 543 TYR cc_start: 0.8086 (m-80) cc_final: 0.7878 (m-80) REVERT: B 559 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: C 78 HIS cc_start: 0.5965 (p-80) cc_final: 0.5732 (p-80) REVERT: C 97 GLU cc_start: 0.7231 (tp30) cc_final: 0.6995 (tp30) REVERT: C 152 ASN cc_start: 0.7798 (m110) cc_final: 0.7244 (p0) REVERT: C 207 GLN cc_start: 0.5026 (pm20) cc_final: 0.4327 (pm20) REVERT: C 288 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8332 (ttpp) REVERT: C 301 THR cc_start: 0.8592 (m) cc_final: 0.8339 (m) outliers start: 68 outliers final: 21 residues processed: 241 average time/residue: 1.4235 time to fit residues: 372.0224 Evaluate side-chains 165 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 40 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 0.0020 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 147 optimal weight: 9.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 380 GLN A 584 ASN B 14 GLN B 335 ASN B 382 ASN B 409 GLN B 463 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106885 restraints weight = 21819.282| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.81 r_work: 0.3271 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13862 Z= 0.149 Angle : 0.547 6.993 18704 Z= 0.280 Chirality : 0.044 0.162 2087 Planarity : 0.004 0.041 2388 Dihedral : 6.959 139.926 1813 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.13 % Allowed : 16.67 % Favored : 79.20 % 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: -1.29 (0.20), residues: 1653 helix: 0.04 (0.20), residues: 629 sheet: -1.38 (0.26), residues: 382 loop : -1.27 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 285 HIS 0.005 0.001 HIS A 463 PHE 0.018 0.001 PHE A 104 TYR 0.019 0.001 TYR B 504 ARG 0.004 0.001 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 582) hydrogen bonds : angle 5.03545 ( 1650) covalent geometry : bond 0.00344 (13862) covalent geometry : angle 0.54745 (18704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 155 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8467 (mp) REVERT: A 77 ILE cc_start: 0.9316 (mt) cc_final: 0.9105 (mp) REVERT: A 165 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: A 166 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6231 (tpm-80) REVERT: A 188 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8554 (ttpt) REVERT: A 262 GLU cc_start: 0.6649 (mm-30) cc_final: 0.6119 (mm-30) REVERT: A 339 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8906 (tt) REVERT: A 352 ASP cc_start: 0.7580 (t0) cc_final: 0.7337 (t0) REVERT: A 384 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8121 (pt) REVERT: A 532 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7138 (mp0) REVERT: A 559 GLU cc_start: 0.7717 (tt0) cc_final: 0.6829 (mt-10) REVERT: B 548 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7927 (tppt) REVERT: B 656 GLU cc_start: 0.7682 (pp20) cc_final: 0.7376 (pp20) REVERT: C 68 ASP cc_start: 0.8369 (t0) cc_final: 0.7994 (t0) REVERT: C 78 HIS cc_start: 0.5908 (p-80) cc_final: 0.5650 (p-80) REVERT: C 97 GLU cc_start: 0.7246 (tp30) cc_final: 0.6885 (tp30) REVERT: C 288 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8268 (ttpp) REVERT: D 306 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7105 (pm20) outliers start: 62 outliers final: 21 residues processed: 205 average time/residue: 1.3274 time to fit residues: 296.9592 Evaluate side-chains 160 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 106 optimal weight: 0.0040 chunk 159 optimal weight: 0.0970 chunk 144 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 135 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 380 GLN A 381 GLN B 14 GLN B 276 ASN B 335 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109367 restraints weight = 21688.935| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.81 r_work: 0.3314 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13862 Z= 0.095 Angle : 0.501 6.985 18704 Z= 0.258 Chirality : 0.042 0.160 2087 Planarity : 0.003 0.041 2388 Dihedral : 6.797 134.923 1813 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.73 % Allowed : 18.87 % Favored : 78.40 % 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: -0.92 (0.20), residues: 1653 helix: 0.48 (0.21), residues: 630 sheet: -1.33 (0.26), residues: 384 loop : -1.10 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 242 HIS 0.003 0.001 HIS B 463 PHE 0.017 0.001 PHE A 104 TYR 0.015 0.001 TYR B 504 ARG 0.003 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 582) hydrogen bonds : angle 4.80278 ( 1650) covalent geometry : bond 0.00204 (13862) covalent geometry : angle 0.50136 (18704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8434 (mp) REVERT: A 165 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: A 188 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8502 (ttpt) REVERT: A 262 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6312 (mm-30) REVERT: A 339 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 352 ASP cc_start: 0.7593 (t0) cc_final: 0.7345 (t0) REVERT: A 430 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: A 532 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7112 (mp0) REVERT: A 559 GLU cc_start: 0.7721 (tt0) cc_final: 0.6922 (mt-10) REVERT: B 349 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7533 (mm-30) REVERT: B 427 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: B 548 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7996 (ttpt) REVERT: B 559 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: C 78 HIS cc_start: 0.5886 (p-80) cc_final: 0.5642 (p-80) REVERT: C 279 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7980 (tppt) REVERT: C 288 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8559 (tttt) REVERT: D 306 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7069 (pm20) outliers start: 41 outliers final: 15 residues processed: 188 average time/residue: 1.2715 time to fit residues: 262.3461 Evaluate side-chains 154 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 12 optimal weight: 0.0370 chunk 116 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN A 380 GLN A 381 GLN B 335 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 463 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109205 restraints weight = 21744.970| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.82 r_work: 0.3313 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13862 Z= 0.097 Angle : 0.491 7.179 18704 Z= 0.253 Chirality : 0.042 0.156 2087 Planarity : 0.003 0.039 2388 Dihedral : 6.740 135.374 1813 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.73 % Allowed : 19.00 % Favored : 78.27 % 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: -0.66 (0.21), residues: 1653 helix: 0.70 (0.21), residues: 632 sheet: -1.22 (0.26), residues: 383 loop : -0.94 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 9 HIS 0.003 0.000 HIS B 463 PHE 0.016 0.001 PHE B 6 TYR 0.012 0.001 TYR B 504 ARG 0.004 0.000 ARG B 575 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 582) hydrogen bonds : angle 4.63750 ( 1650) covalent geometry : bond 0.00216 (13862) covalent geometry : angle 0.49140 (18704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8538 (t) REVERT: A 29 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 165 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: A 262 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6367 (mm-30) REVERT: A 339 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8862 (tt) REVERT: A 352 ASP cc_start: 0.7564 (t0) cc_final: 0.7309 (t0) REVERT: A 430 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: A 532 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7129 (mp0) REVERT: A 559 GLU cc_start: 0.7687 (tt0) cc_final: 0.6949 (mt-10) REVERT: B 349 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7404 (mm-30) REVERT: B 427 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: B 559 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: C 78 HIS cc_start: 0.5986 (p-80) cc_final: 0.5714 (p-80) REVERT: C 108 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6504 (mm-40) REVERT: C 279 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7812 (tppt) REVERT: C 288 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8558 (tttt) REVERT: C 309 HIS cc_start: 0.6851 (m-70) cc_final: 0.6639 (m170) REVERT: D 306 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7107 (pm20) outliers start: 41 outliers final: 15 residues processed: 190 average time/residue: 1.3994 time to fit residues: 290.2172 Evaluate side-chains 162 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.083 > 50: distance: 40 - 227: 21.233 distance: 43 - 224: 12.824 distance: 55 - 213: 19.661 distance: 58 - 210: 8.484 distance: 70 - 200: 28.987 distance: 73 - 197: 12.258 distance: 105 - 209: 28.823 distance: 108 - 217: 14.754 distance: 119 - 220: 6.826 distance: 122 - 232: 8.193 distance: 173 - 174: 12.781 distance: 174 - 175: 14.473 distance: 174 - 177: 15.950 distance: 175 - 176: 20.160 distance: 175 - 179: 9.613 distance: 177 - 178: 7.340 distance: 179 - 180: 27.299 distance: 180 - 181: 15.843 distance: 180 - 183: 10.923 distance: 181 - 182: 22.419 distance: 181 - 190: 15.974 distance: 183 - 184: 8.430 distance: 184 - 185: 14.406 distance: 184 - 186: 16.116 distance: 185 - 187: 10.770 distance: 186 - 188: 12.003 distance: 187 - 189: 15.704 distance: 188 - 189: 11.954 distance: 190 - 191: 10.319 distance: 191 - 192: 17.468 distance: 191 - 194: 21.253 distance: 192 - 193: 19.229 distance: 192 - 197: 12.115 distance: 194 - 195: 13.807 distance: 194 - 196: 20.555 distance: 198 - 199: 10.991 distance: 198 - 201: 18.534 distance: 199 - 200: 18.546 distance: 199 - 206: 17.704 distance: 201 - 202: 19.518 distance: 202 - 203: 14.578 distance: 203 - 204: 25.079 distance: 204 - 205: 16.437 distance: 206 - 207: 4.887 distance: 207 - 208: 16.338 distance: 208 - 209: 27.545 distance: 208 - 210: 3.050 distance: 210 - 211: 13.971 distance: 211 - 212: 14.500 distance: 211 - 214: 12.813 distance: 212 - 213: 8.478 distance: 212 - 217: 13.789 distance: 214 - 215: 17.239 distance: 214 - 216: 14.872 distance: 217 - 218: 8.729 distance: 218 - 219: 7.077 distance: 218 - 221: 17.802 distance: 219 - 220: 10.417 distance: 219 - 224: 15.166 distance: 221 - 223: 19.932 distance: 224 - 225: 12.109 distance: 225 - 226: 11.681 distance: 225 - 228: 28.515 distance: 226 - 227: 19.655 distance: 226 - 232: 20.274 distance: 228 - 229: 14.185 distance: 229 - 230: 26.700 distance: 229 - 231: 17.293 distance: 232 - 233: 17.110 distance: 233 - 234: 33.108 distance: 233 - 236: 10.447 distance: 234 - 235: 20.747 distance: 234 - 238: 27.632 distance: 236 - 237: 19.000 distance: 238 - 239: 20.877 distance: 239 - 240: 22.593 distance: 239 - 242: 7.620 distance: 240 - 241: 25.804 distance: 240 - 247: 16.542 distance: 242 - 243: 16.485 distance: 243 - 244: 29.111 distance: 244 - 245: 16.141 distance: 244 - 246: 23.395