Starting phenix.real_space_refine on Sun Aug 4 05:22:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/08_2024/7whm_32504.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/08_2024/7whm_32504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/08_2024/7whm_32504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/08_2024/7whm_32504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/08_2024/7whm_32504.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/08_2024/7whm_32504.cif" } resolution = 2.7 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 6048 2.51 5 N 1706 2.21 5 O 1857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A ASP 774": "OD1" <-> "OD2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A ARG 890": "NH1" <-> "NH2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A ARG 925": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "A ARG 1080": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1147": "NH1" <-> "NH2" Residue "A PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1198": "NH1" <-> "NH2" Residue "A ARG 1212": "NH1" <-> "NH2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ARG 1220": "NH1" <-> "NH2" Residue "A ARG 1232": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9650 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1214, 9650 Classifications: {'peptide': 1214} Link IDs: {'PCIS': 4, 'PTRANS': 38, 'TRANS': 1171} Time building chain proxies: 5.76, per 1000 atoms: 0.60 Number of scatterers: 9650 At special positions: 0 Unit cell: (110.448, 128.502, 133.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1857 8.00 N 1706 7.00 C 6048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.8 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 37.7% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 28 through 53 Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 306 through 338 removed outlier: 3.723A pdb=" N HIS A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 372 removed outlier: 3.534A pdb=" N ARG A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.562A pdb=" N ARG A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 658 removed outlier: 3.734A pdb=" N ASN A 655 " --> pdb=" O MET A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 688 Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.324A pdb=" N ARG A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 769 Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'A' and resid 778 through 796 Processing helix chain 'A' and resid 800 through 814 removed outlier: 3.739A pdb=" N ILE A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 835 Processing helix chain 'A' and resid 835 through 850 Processing helix chain 'A' and resid 852 through 861 removed outlier: 4.174A pdb=" N GLY A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 885 Processing helix chain 'A' and resid 887 through 892 Processing helix chain 'A' and resid 897 through 901 Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 909 through 923 Processing helix chain 'A' and resid 924 through 928 Processing helix chain 'A' and resid 932 through 937 Processing helix chain 'A' and resid 979 through 994 Processing helix chain 'A' and resid 1074 through 1087 Processing helix chain 'A' and resid 1094 through 1105 Processing helix chain 'A' and resid 1123 through 1136 removed outlier: 3.692A pdb=" N LEU A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1148 through 1161 removed outlier: 4.027A pdb=" N PHE A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A1153 " --> pdb=" O CYS A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1193 removed outlier: 4.154A pdb=" N ALA A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1220 removed outlier: 3.522A pdb=" N ARG A1220 " --> pdb=" O LYS A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1236 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.934A pdb=" N ASN A 105 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 235 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN A 260 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N SER A 237 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL A 258 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS A 239 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL A 256 " --> pdb=" O HIS A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.761A pdb=" N VAL A 296 " --> pdb=" O LYS A1109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 181 removed outlier: 6.390A pdb=" N ASP A 155 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR A 149 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU A 157 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 139 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN A 124 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG A 125 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 284 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 127 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 206 removed outlier: 4.176A pdb=" N ASN A1053 " --> pdb=" O ILE A1062 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE A1062 " --> pdb=" O ASN A1053 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 300 " --> pdb=" O ILE A1063 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ARG A1065 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 206 removed outlier: 6.697A pdb=" N SER A1016 " --> pdb=" O GLU A1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 380 through 395 removed outlier: 5.516A pdb=" N ARG A 382 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A 738 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU A 384 " --> pdb=" O ALA A 736 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA A 736 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG A 386 " --> pdb=" O TRP A 734 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TRP A 734 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP A 388 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY A 732 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR A 725 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR A 570 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL A 727 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU A 568 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 729 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 566 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N HIS A 731 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU A 564 " --> pdb=" O HIS A 731 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 733 " --> pdb=" O GLY A 562 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY A 562 " --> pdb=" O ASN A 733 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER A 735 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR A 560 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 573 " --> pdb=" O TYR A 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 409 removed outlier: 6.814A pdb=" N GLN A 435 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE A 676 " --> pdb=" O GLN A 435 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG A 437 " --> pdb=" O PHE A 676 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL A 678 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 439 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR A 673 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A 667 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 458 removed outlier: 5.587A pdb=" N ASN A 449 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN A 472 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER A 451 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR A 470 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE A 453 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE A 468 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN A 455 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 466 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 545 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER A 469 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL A 543 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ARG A 471 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE A 541 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 604 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 545 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 602 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU A 547 " --> pdb=" O CYS A 600 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N CYS A 600 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 549 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 598 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 502 removed outlier: 6.989A pdb=" N THR A 510 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 529 through 531 Processing sheet with id=AB2, first strand: chain 'A' and resid 864 through 865 removed outlier: 6.561A pdb=" N ASN A 864 " --> pdb=" O GLU A1119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 462 hydrogen bonds defined for protein. 1320 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: 3.93 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3261 1.34 - 1.45: 1325 1.45 - 1.57: 5168 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9828 Sorted by residual: bond pdb=" CB THR A1007 " pdb=" CG2 THR A1007 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.54e+00 bond pdb=" CG1 ILE A1048 " pdb=" CD1 ILE A1048 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.29e+00 bond pdb=" CA GLY A 204 " pdb=" C GLY A 204 " ideal model delta sigma weight residual 1.520 1.500 0.020 1.39e-02 5.18e+03 2.09e+00 bond pdb=" CB ASP A 182 " pdb=" CG ASP A 182 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.88e+00 bond pdb=" CB ASN A1148 " pdb=" CG ASN A1148 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.74e+00 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 98.93 - 105.94: 165 105.94 - 112.96: 5387 112.96 - 119.98: 3216 119.98 - 127.00: 4469 127.00 - 134.02: 88 Bond angle restraints: 13325 Sorted by residual: angle pdb=" C THR A 133 " pdb=" N THR A 134 " pdb=" CA THR A 134 " ideal model delta sigma weight residual 122.74 129.54 -6.80 2.44e+00 1.68e-01 7.77e+00 angle pdb=" C TYR A 710 " pdb=" N GLN A 711 " pdb=" CA GLN A 711 " ideal model delta sigma weight residual 122.61 126.39 -3.78 1.56e+00 4.11e-01 5.86e+00 angle pdb=" N LEU A 745 " pdb=" CA LEU A 745 " pdb=" C LEU A 745 " ideal model delta sigma weight residual 109.81 115.13 -5.32 2.21e+00 2.05e-01 5.81e+00 angle pdb=" CA MET A 955 " pdb=" CB MET A 955 " pdb=" CG MET A 955 " ideal model delta sigma weight residual 114.10 118.82 -4.72 2.00e+00 2.50e-01 5.57e+00 angle pdb=" C TYR A 615 " pdb=" N LEU A 616 " pdb=" CA LEU A 616 " ideal model delta sigma weight residual 120.28 123.63 -3.35 1.44e+00 4.82e-01 5.42e+00 ... (remaining 13320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5400 17.65 - 35.30: 453 35.30 - 52.96: 78 52.96 - 70.61: 19 70.61 - 88.26: 8 Dihedral angle restraints: 5958 sinusoidal: 2406 harmonic: 3552 Sorted by residual: dihedral pdb=" CA ILE A 692 " pdb=" C ILE A 692 " pdb=" N SER A 693 " pdb=" CA SER A 693 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA PRO A 700 " pdb=" C PRO A 700 " pdb=" N VAL A 701 " pdb=" CA VAL A 701 " ideal model delta harmonic sigma weight residual 180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TYR A 706 " pdb=" C TYR A 706 " pdb=" N ALA A 707 " pdb=" CA ALA A 707 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 969 0.040 - 0.081: 378 0.081 - 0.121: 150 0.121 - 0.161: 18 0.161 - 0.202: 2 Chirality restraints: 1517 Sorted by residual: chirality pdb=" CB VAL A 904 " pdb=" CA VAL A 904 " pdb=" CG1 VAL A 904 " pdb=" CG2 VAL A 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR A1007 " pdb=" CA THR A1007 " pdb=" OG1 THR A1007 " pdb=" CG2 THR A1007 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA VAL A 113 " pdb=" N VAL A 113 " pdb=" C VAL A 113 " pdb=" CB VAL A 113 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1514 not shown) Planarity restraints: 1737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 134 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 135 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 398 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 399 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 149 " -0.009 2.00e-02 2.50e+03 9.94e-03 1.98e+00 pdb=" CG TYR A 149 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 149 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 149 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 149 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 149 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 149 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 149 " 0.000 2.00e-02 2.50e+03 ... (remaining 1734 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 240 2.70 - 3.25: 9086 3.25 - 3.80: 15015 3.80 - 4.35: 19729 4.35 - 4.90: 33490 Nonbonded interactions: 77560 Sorted by model distance: nonbonded pdb=" O THR A 84 " pdb=" NH1 ARG A 960 " model vdw 2.155 3.120 nonbonded pdb=" O LEU A 482 " pdb=" NE2 GLN A 531 " model vdw 2.222 3.120 nonbonded pdb=" OH TYR A 470 " pdb=" OE1 GLN A 472 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP A 309 " pdb=" NH2 ARG A 312 " model vdw 2.262 3.120 nonbonded pdb=" O TYR A 72 " pdb=" OG1 THR A 75 " model vdw 2.313 3.040 ... (remaining 77555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.250 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.006 0.059 9828 Z= 0.414 Angle : 0.637 6.811 13325 Z= 0.364 Chirality : 0.048 0.202 1517 Planarity : 0.004 0.040 1737 Dihedral : 13.847 88.259 3666 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.15 (0.23), residues: 1212 helix: 1.29 (0.25), residues: 416 sheet: 0.04 (0.29), residues: 292 loop : -0.82 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1099 HIS 0.008 0.001 HIS A 195 PHE 0.022 0.002 PHE A 101 TYR 0.023 0.002 TYR A 149 ARG 0.010 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.099 Fit side-chains REVERT: A 679 GLU cc_start: 0.7732 (tt0) cc_final: 0.7424 (tt0) REVERT: A 733 ASN cc_start: 0.6813 (p0) cc_final: 0.6593 (p0) REVERT: A 1186 MET cc_start: 0.9029 (tpt) cc_final: 0.8820 (tpt) outliers start: 0 outliers final: 1 residues processed: 155 average time/residue: 1.5585 time to fit residues: 255.8341 Evaluate side-chains 137 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1190 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 260 GLN A1139 GLN A1179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9828 Z= 0.240 Angle : 0.546 6.723 13325 Z= 0.296 Chirality : 0.045 0.160 1517 Planarity : 0.004 0.041 1737 Dihedral : 5.074 52.280 1352 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.23 % Allowed : 7.15 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.65 (0.24), residues: 1212 helix: 2.01 (0.25), residues: 402 sheet: 0.35 (0.31), residues: 271 loop : -0.73 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1099 HIS 0.004 0.001 HIS A 195 PHE 0.012 0.002 PHE A 128 TYR 0.015 0.002 TYR A 72 ARG 0.011 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.104 Fit side-chains REVERT: A 161 LYS cc_start: 0.8556 (tmtp) cc_final: 0.8325 (tmtp) REVERT: A 257 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: A 437 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6446 (ptt180) REVERT: A 638 THR cc_start: 0.8912 (t) cc_final: 0.8557 (m) REVERT: A 679 GLU cc_start: 0.7603 (tt0) cc_final: 0.7208 (tt0) REVERT: A 780 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8252 (mptt) REVERT: A 1131 ASP cc_start: 0.8552 (m-30) cc_final: 0.8347 (m-30) REVERT: A 1212 ARG cc_start: 0.7513 (mtm110) cc_final: 0.7258 (mtm-85) outliers start: 24 outliers final: 9 residues processed: 154 average time/residue: 1.4085 time to fit residues: 230.4587 Evaluate side-chains 155 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1190 MET Chi-restraints excluded: chain A residue 1216 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A1139 GLN A1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9828 Z= 0.188 Angle : 0.495 5.976 13325 Z= 0.268 Chirality : 0.043 0.155 1517 Planarity : 0.004 0.041 1737 Dihedral : 4.592 28.572 1352 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 8.64 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.97 (0.24), residues: 1212 helix: 2.28 (0.25), residues: 406 sheet: 0.66 (0.32), residues: 256 loop : -0.63 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1099 HIS 0.004 0.001 HIS A 317 PHE 0.012 0.001 PHE A1003 TYR 0.017 0.001 TYR A 674 ARG 0.004 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.072 Fit side-chains REVERT: A 161 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8259 (tmtp) REVERT: A 257 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: A 351 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: A 594 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: A 628 GLU cc_start: 0.4963 (pt0) cc_final: 0.3907 (tp30) REVERT: A 638 THR cc_start: 0.8908 (t) cc_final: 0.8603 (m) REVERT: A 672 MET cc_start: 0.6695 (mmt) cc_final: 0.6390 (mmt) REVERT: A 679 GLU cc_start: 0.7487 (tt0) cc_final: 0.7150 (tt0) outliers start: 23 outliers final: 6 residues processed: 155 average time/residue: 1.4626 time to fit residues: 240.5807 Evaluate side-chains 154 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1063 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 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 260 GLN A 484 GLN A1089 GLN A1139 GLN A1179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9828 Z= 0.159 Angle : 0.471 5.691 13325 Z= 0.255 Chirality : 0.043 0.153 1517 Planarity : 0.003 0.041 1737 Dihedral : 4.315 21.200 1349 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.32 % Allowed : 10.12 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.14 (0.24), residues: 1212 helix: 2.46 (0.25), residues: 408 sheet: 0.68 (0.32), residues: 260 loop : -0.54 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1099 HIS 0.004 0.001 HIS A 452 PHE 0.013 0.001 PHE A 676 TYR 0.019 0.001 TYR A 462 ARG 0.004 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.088 Fit side-chains REVERT: A 161 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8218 (tmtp) REVERT: A 257 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: A 351 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: A 594 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: A 628 GLU cc_start: 0.4879 (pt0) cc_final: 0.3932 (tp30) REVERT: A 638 THR cc_start: 0.8895 (t) cc_final: 0.8609 (m) REVERT: A 651 MET cc_start: 0.8313 (mpt) cc_final: 0.8093 (mtt) REVERT: A 841 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.7268 (mtp180) outliers start: 25 outliers final: 8 residues processed: 152 average time/residue: 1.4875 time to fit residues: 240.6648 Evaluate side-chains 155 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.7649 > 50: distance: 22 - 24: 20.878 distance: 24 - 25: 4.578 distance: 25 - 26: 5.068 distance: 25 - 28: 16.864 distance: 26 - 27: 22.392 distance: 26 - 29: 47.370 distance: 29 - 30: 25.321 distance: 30 - 31: 24.575 distance: 30 - 33: 8.638 distance: 31 - 32: 11.786 distance: 31 - 38: 13.515 distance: 33 - 34: 6.516 distance: 34 - 35: 45.061 distance: 35 - 36: 6.362 distance: 35 - 37: 10.210 distance: 38 - 39: 19.410 distance: 38 - 44: 12.952 distance: 39 - 40: 10.900 distance: 39 - 42: 14.889 distance: 40 - 41: 16.085 distance: 40 - 45: 29.006 distance: 41 - 65: 20.216 distance: 42 - 43: 16.626 distance: 43 - 44: 17.041 distance: 45 - 46: 14.196 distance: 46 - 47: 23.049 distance: 46 - 49: 25.216 distance: 47 - 48: 10.728 distance: 47 - 53: 32.340 distance: 48 - 74: 15.723 distance: 49 - 50: 14.432 distance: 50 - 51: 22.454 distance: 50 - 52: 14.726 distance: 53 - 54: 33.801 distance: 54 - 55: 11.654 distance: 54 - 57: 21.495 distance: 55 - 56: 12.423 distance: 55 - 65: 16.286 distance: 57 - 58: 9.151 distance: 58 - 59: 11.521 distance: 58 - 60: 5.887 distance: 59 - 61: 11.082 distance: 60 - 62: 10.167 distance: 61 - 63: 8.384 distance: 62 - 63: 14.888 distance: 63 - 64: 5.367 distance: 66 - 67: 17.408 distance: 66 - 69: 22.323 distance: 67 - 68: 21.193 distance: 67 - 74: 19.025 distance: 69 - 70: 25.821 distance: 70 - 71: 8.900 distance: 71 - 72: 27.885 distance: 72 - 73: 17.701 distance: 74 - 75: 19.878 distance: 75 - 76: 37.965 distance: 75 - 78: 11.907 distance: 76 - 77: 32.790 distance: 76 - 82: 17.006 distance: 78 - 79: 9.689 distance: 79 - 80: 8.645 distance: 79 - 81: 5.646 distance: 82 - 83: 12.801 distance: 83 - 84: 20.390 distance: 83 - 86: 5.551 distance: 84 - 85: 30.583 distance: 84 - 90: 25.518 distance: 86 - 87: 9.656 distance: 87 - 88: 14.970 distance: 87 - 89: 10.021 distance: 90 - 91: 13.991 distance: 91 - 92: 20.976 distance: 91 - 94: 24.395 distance: 92 - 93: 33.741 distance: 92 - 99: 20.214 distance: 94 - 95: 13.524 distance: 95 - 96: 16.099 distance: 96 - 97: 26.710 distance: 97 - 98: 31.180 distance: 99 - 100: 17.455 distance: 100 - 101: 46.298 distance: 100 - 103: 10.189 distance: 101 - 102: 27.844 distance: 101 - 106: 24.676 distance: 102 - 127: 13.804 distance: 103 - 104: 31.595 distance: 103 - 105: 42.361