Starting phenix.real_space_refine on Sun May 18 10:37:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl3_25190/05_2025/7sl3_25190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl3_25190/05_2025/7sl3_25190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sl3_25190/05_2025/7sl3_25190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl3_25190/05_2025/7sl3_25190.map" model { file = "/net/cci-nas-00/data/ceres_data/7sl3_25190/05_2025/7sl3_25190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl3_25190/05_2025/7sl3_25190_neut.cif" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 8898 2.51 5 N 2408 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14016 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "B" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6629 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 774} Chain breaks: 6 Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "D" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "E" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 8.19, per 1000 atoms: 0.58 Number of scatterers: 14016 At special positions: 0 Unit cell: (139.32, 115.56, 174.96, 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 112 16.00 O 2598 8.00 N 2408 7.00 C 8898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " distance=2.03 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 34 sheets defined 17.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.977A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 24' Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.733A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.817A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.593A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.801A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.695A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.521A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.502A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.962A pdb=" N PHE A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 645' Processing helix chain 'A' and resid 691 through 716 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 18 through 24 removed outlier: 4.066A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 24' Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.719A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.837A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.584A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.807A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.686A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.511A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.506A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.028A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 690 through 716 removed outlier: 5.283A pdb=" N LYS B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.768A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.745A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.536A pdb=" N GLU E 17 " --> pdb=" O TYR E 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 13 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 3.502A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.844A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.550A pdb=" N LEU A 368 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.772A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.619A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 601 through 607 removed outlier: 5.897A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 613 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 770 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.045A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 630 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 632 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 762 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.045A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 824 removed outlier: 3.553A pdb=" N VAL A 830 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 858 through 864 removed outlier: 6.896A pdb=" N THR A 891 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 847 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 889 " --> pdb=" O TYR A 847 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 849 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A 887 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 851 " --> pdb=" O SER A 885 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 885 " --> pdb=" O TYR A 851 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A 853 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN A 883 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 882 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.598A pdb=" N LEU B 36 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.840A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.580A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.718A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC7, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC9, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.543A pdb=" N LEU B 368 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD2, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.735A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.548A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.599A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.509A pdb=" N GLU B 762 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD7, first strand: chain 'B' and resid 858 through 864 removed outlier: 6.847A pdb=" N THR B 891 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 847 " --> pdb=" O ARG B 889 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 889 " --> pdb=" O TYR B 847 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 849 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 887 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR B 851 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER B 885 " --> pdb=" O TYR B 851 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG B 853 " --> pdb=" O ASN B 883 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN B 883 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 882 " --> pdb=" O VAL B 907 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 858 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: 5.01 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4591 1.34 - 1.46: 3333 1.46 - 1.58: 6298 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14358 Sorted by residual: bond pdb=" CA THR B 690 " pdb=" CB THR B 690 " ideal model delta sigma weight residual 1.518 1.540 -0.023 2.08e-02 2.31e+03 1.18e+00 bond pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CA LYS B 559 " pdb=" CB LYS B 559 " ideal model delta sigma weight residual 1.519 1.537 -0.017 1.73e-02 3.34e+03 9.81e-01 bond pdb=" CA CYS B 687 " pdb=" C CYS B 687 " ideal model delta sigma weight residual 1.524 1.516 0.008 8.10e-03 1.52e+04 9.47e-01 bond pdb=" CA LYS A 559 " pdb=" CB LYS A 559 " ideal model delta sigma weight residual 1.519 1.536 -0.016 1.73e-02 3.34e+03 9.03e-01 ... (remaining 14353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 19248 2.20 - 4.40: 198 4.40 - 6.59: 11 6.59 - 8.79: 1 8.79 - 10.99: 2 Bond angle restraints: 19460 Sorted by residual: angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 132.53 -10.99 1.91e+00 2.74e-01 3.31e+01 angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C THR B 690 " pdb=" CA THR B 690 " pdb=" CB THR B 690 " ideal model delta sigma weight residual 115.79 109.56 6.23 1.19e+00 7.06e-01 2.74e+01 angle pdb=" N ASP A 691 " pdb=" CA ASP A 691 " pdb=" C ASP A 691 " ideal model delta sigma weight residual 113.41 109.26 4.15 1.22e+00 6.72e-01 1.16e+01 angle pdb=" N SER B 692 " pdb=" CA SER B 692 " pdb=" C SER B 692 " ideal model delta sigma weight residual 113.19 109.62 3.57 1.19e+00 7.06e-01 8.98e+00 ... (remaining 19455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7931 17.94 - 35.87: 628 35.87 - 53.81: 114 53.81 - 71.74: 29 71.74 - 89.68: 10 Dihedral angle restraints: 8712 sinusoidal: 3640 harmonic: 5072 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -148.27 62.27 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -147.43 61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 147.12 -54.12 1 1.00e+01 1.00e-02 3.97e+01 ... (remaining 8709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1357 0.034 - 0.068: 490 0.068 - 0.101: 164 0.101 - 0.135: 95 0.135 - 0.169: 4 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CB THR B 690 " pdb=" CA THR B 690 " pdb=" OG1 THR B 690 " pdb=" CG2 THR B 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB THR A 690 " pdb=" CA THR A 690 " pdb=" OG1 THR A 690 " pdb=" CG2 THR A 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 2107 not shown) Planarity restraints: 2516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C THR B 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR B 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 580 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C THR A 580 " -0.039 2.00e-02 2.50e+03 pdb=" O THR A 580 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 581 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 836 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 837 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 837 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 837 " 0.017 5.00e-02 4.00e+02 ... (remaining 2513 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2332 2.77 - 3.30: 13128 3.30 - 3.84: 22468 3.84 - 4.37: 26556 4.37 - 4.90: 45564 Nonbonded interactions: 110048 Sorted by model distance: nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.238 3.040 nonbonded pdb=" NH2 ARG A 14 " pdb=" O VAL B 715 " model vdw 2.241 3.120 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.244 3.040 nonbonded pdb=" O VAL A 715 " pdb=" NH2 ARG B 14 " model vdw 2.245 3.120 nonbonded pdb=" NE2 GLN A 790 " pdb=" O ASP A 794 " model vdw 2.246 3.120 ... (remaining 110043 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.520 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.002 0.039 14398 Z= 0.111 Angle : 0.539 10.991 19540 Z= 0.288 Chirality : 0.043 0.169 2110 Planarity : 0.003 0.031 2516 Dihedral : 13.247 89.680 5316 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.35 % Favored : 93.41 % Rotamer: Outliers : 0.32 % Allowed : 0.32 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.71 (0.21), residues: 1700 helix: -0.32 (0.36), residues: 222 sheet: 0.84 (0.30), residues: 334 loop : -0.95 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 412 HIS 0.003 0.000 HIS A 440 PHE 0.013 0.001 PHE B 778 TYR 0.014 0.001 TYR B 581 ARG 0.003 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.23714 ( 333) hydrogen bonds : angle 8.15140 ( 858) SS BOND : bond 0.00193 ( 40) SS BOND : angle 0.97940 ( 80) covalent geometry : bond 0.00239 (14358) covalent geometry : angle 0.53683 (19460) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: B 687 CYS cc_start: 0.2703 (OUTLIER) cc_final: 0.2494 (m) REVERT: F 17 GLU cc_start: 0.7541 (mp0) cc_final: 0.7209 (mp0) outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.2480 time to fit residues: 28.3331 Evaluate side-chains 55 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 689 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 100 optimal weight: 30.0000 chunk 156 optimal weight: 0.4980 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.104374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070968 restraints weight = 40058.781| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.39 r_work: 0.3145 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14398 Z= 0.116 Angle : 0.529 6.638 19540 Z= 0.279 Chirality : 0.044 0.192 2110 Planarity : 0.003 0.029 2516 Dihedral : 4.840 55.746 1905 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.06 % Favored : 93.76 % Rotamer: Outliers : 0.25 % Allowed : 4.11 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.56 (0.21), residues: 1700 helix: 0.37 (0.37), residues: 212 sheet: 0.89 (0.30), residues: 322 loop : -0.93 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 412 HIS 0.004 0.001 HIS A 440 PHE 0.011 0.001 PHE A 707 TYR 0.014 0.001 TYR E 14 ARG 0.006 0.000 ARG A 782 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 333) hydrogen bonds : angle 6.10574 ( 858) SS BOND : bond 0.00289 ( 40) SS BOND : angle 0.75663 ( 80) covalent geometry : bond 0.00272 (14358) covalent geometry : angle 0.52793 (19460) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 691 ASP cc_start: 0.8120 (p0) cc_final: 0.7759 (p0) REVERT: A 808 MET cc_start: 0.5970 (ptt) cc_final: 0.5670 (mmp) REVERT: E 17 GLU cc_start: 0.7798 (mp0) cc_final: 0.7439 (mp0) REVERT: F 14 TYR cc_start: 0.7911 (t80) cc_final: 0.7256 (t80) REVERT: F 17 GLU cc_start: 0.8197 (mp0) cc_final: 0.7767 (mp0) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.2335 time to fit residues: 24.2801 Evaluate side-chains 53 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 130 optimal weight: 0.1980 chunk 170 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 712 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.102631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069011 restraints weight = 40785.714| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.42 r_work: 0.3091 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14398 Z= 0.178 Angle : 0.541 7.102 19540 Z= 0.284 Chirality : 0.045 0.187 2110 Planarity : 0.003 0.033 2516 Dihedral : 4.673 34.038 1900 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 0.32 % Allowed : 7.84 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1700 helix: 0.60 (0.38), residues: 210 sheet: 0.57 (0.30), residues: 342 loop : -0.95 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 412 HIS 0.006 0.001 HIS B 712 PHE 0.012 0.001 PHE B 381 TYR 0.031 0.001 TYR B 581 ARG 0.003 0.000 ARG A 782 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 333) hydrogen bonds : angle 5.74294 ( 858) SS BOND : bond 0.00291 ( 40) SS BOND : angle 1.00263 ( 80) covalent geometry : bond 0.00422 (14358) covalent geometry : angle 0.53779 (19460) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8861 (tpt) cc_final: 0.8616 (tpt) REVERT: A 442 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8277 (ttp) REVERT: A 691 ASP cc_start: 0.8146 (p0) cc_final: 0.7790 (p0) REVERT: A 833 MET cc_start: 0.5057 (mmt) cc_final: 0.4508 (tpt) REVERT: E 14 TYR cc_start: 0.8081 (t80) cc_final: 0.7692 (t80) REVERT: E 17 GLU cc_start: 0.7997 (mp0) cc_final: 0.7619 (mp0) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.2319 time to fit residues: 23.4517 Evaluate side-chains 52 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.101843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.068181 restraints weight = 39650.498| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.40 r_work: 0.3093 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14398 Z= 0.205 Angle : 0.556 8.351 19540 Z= 0.292 Chirality : 0.045 0.183 2110 Planarity : 0.003 0.036 2516 Dihedral : 4.846 33.160 1900 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.76 % Favored : 93.18 % Rotamer: Outliers : 0.57 % Allowed : 9.29 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.77 (0.21), residues: 1700 helix: 0.35 (0.37), residues: 222 sheet: 0.39 (0.29), residues: 346 loop : -1.03 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 412 HIS 0.005 0.001 HIS A 712 PHE 0.012 0.002 PHE B 381 TYR 0.027 0.001 TYR B 581 ARG 0.002 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 333) hydrogen bonds : angle 5.65500 ( 858) SS BOND : bond 0.00319 ( 40) SS BOND : angle 1.23555 ( 80) covalent geometry : bond 0.00486 (14358) covalent geometry : angle 0.55124 (19460) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 1.659 Fit side-chains revert: symmetry clash REVERT: A 442 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8433 (ttp) REVERT: A 691 ASP cc_start: 0.8113 (p0) cc_final: 0.7773 (p0) REVERT: A 833 MET cc_start: 0.5129 (mmt) cc_final: 0.4428 (tpt) REVERT: E 17 GLU cc_start: 0.7950 (mp0) cc_final: 0.7559 (mp0) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.2267 time to fit residues: 24.2068 Evaluate side-chains 56 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 90 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 0.0570 chunk 128 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 145 optimal weight: 40.0000 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.103310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069808 restraints weight = 40051.812| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.45 r_work: 0.3129 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14398 Z= 0.101 Angle : 0.506 7.060 19540 Z= 0.267 Chirality : 0.043 0.211 2110 Planarity : 0.003 0.034 2516 Dihedral : 4.678 33.631 1900 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.59 % Favored : 94.35 % Rotamer: Outliers : 0.57 % Allowed : 10.49 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.69 (0.21), residues: 1700 helix: 0.56 (0.38), residues: 210 sheet: 0.53 (0.29), residues: 342 loop : -1.01 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.003 0.001 HIS A 440 PHE 0.013 0.001 PHE A 707 TYR 0.022 0.001 TYR B 581 ARG 0.002 0.000 ARG A 782 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 333) hydrogen bonds : angle 5.40299 ( 858) SS BOND : bond 0.00253 ( 40) SS BOND : angle 1.01601 ( 80) covalent geometry : bond 0.00240 (14358) covalent geometry : angle 0.50328 (19460) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.9083 (mmm) cc_final: 0.8433 (tpt) REVERT: A 120 GLU cc_start: 0.8214 (tt0) cc_final: 0.8007 (tt0) REVERT: A 691 ASP cc_start: 0.8077 (p0) cc_final: 0.7660 (p0) REVERT: A 833 MET cc_start: 0.5309 (mmt) cc_final: 0.4603 (tpt) REVERT: B 639 GLU cc_start: 0.4011 (mm-30) cc_final: 0.3141 (pm20) REVERT: E 14 TYR cc_start: 0.8104 (t80) cc_final: 0.7633 (t80) REVERT: E 17 GLU cc_start: 0.7945 (mp0) cc_final: 0.7531 (mp0) outliers start: 9 outliers final: 6 residues processed: 65 average time/residue: 0.2337 time to fit residues: 24.9560 Evaluate side-chains 57 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 63 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.100029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066263 restraints weight = 40914.168| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.41 r_work: 0.3046 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 14398 Z= 0.308 Angle : 0.666 9.590 19540 Z= 0.345 Chirality : 0.048 0.236 2110 Planarity : 0.004 0.036 2516 Dihedral : 5.166 36.813 1900 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.63 % Allowed : 11.69 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.08 (0.21), residues: 1700 helix: 0.02 (0.36), residues: 218 sheet: -0.06 (0.28), residues: 364 loop : -1.13 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 183 HIS 0.008 0.002 HIS A 712 PHE 0.020 0.002 PHE B 89 TYR 0.031 0.002 TYR B 581 ARG 0.004 0.001 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.04808 ( 333) hydrogen bonds : angle 5.78539 ( 858) SS BOND : bond 0.00462 ( 40) SS BOND : angle 1.07880 ( 80) covalent geometry : bond 0.00728 (14358) covalent geometry : angle 0.66408 (19460) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9029 (mp) REVERT: A 691 ASP cc_start: 0.8172 (p0) cc_final: 0.7749 (p0) REVERT: B 344 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9032 (mp) outliers start: 10 outliers final: 4 residues processed: 66 average time/residue: 0.2637 time to fit residues: 28.3650 Evaluate side-chains 58 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 118 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 139 optimal weight: 0.0980 chunk 106 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.101467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067922 restraints weight = 40088.150| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.41 r_work: 0.3091 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14398 Z= 0.137 Angle : 0.537 6.442 19540 Z= 0.282 Chirality : 0.044 0.198 2110 Planarity : 0.003 0.031 2516 Dihedral : 4.866 32.427 1900 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.51 % Allowed : 12.14 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.21), residues: 1700 helix: 0.24 (0.37), residues: 222 sheet: -0.06 (0.28), residues: 370 loop : -1.07 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 412 HIS 0.003 0.001 HIS B 440 PHE 0.017 0.001 PHE A 778 TYR 0.021 0.001 TYR A 512 ARG 0.003 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 333) hydrogen bonds : angle 5.47344 ( 858) SS BOND : bond 0.00259 ( 40) SS BOND : angle 0.74747 ( 80) covalent geometry : bond 0.00325 (14358) covalent geometry : angle 0.53587 (19460) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8897 (mp) REVERT: A 691 ASP cc_start: 0.8119 (p0) cc_final: 0.7678 (p0) REVERT: B 344 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8904 (mp) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.2547 time to fit residues: 25.1835 Evaluate side-chains 55 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 161 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.101413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.067985 restraints weight = 39868.493| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.40 r_work: 0.3092 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14398 Z= 0.137 Angle : 0.526 6.592 19540 Z= 0.275 Chirality : 0.044 0.197 2110 Planarity : 0.003 0.030 2516 Dihedral : 4.720 32.835 1900 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.70 % Allowed : 12.20 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.87 (0.21), residues: 1700 helix: 0.26 (0.37), residues: 222 sheet: 0.19 (0.29), residues: 364 loop : -1.05 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 412 HIS 0.003 0.001 HIS B 860 PHE 0.013 0.001 PHE A 778 TYR 0.019 0.001 TYR A 512 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 333) hydrogen bonds : angle 5.33583 ( 858) SS BOND : bond 0.00249 ( 40) SS BOND : angle 0.69766 ( 80) covalent geometry : bond 0.00329 (14358) covalent geometry : angle 0.52540 (19460) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8912 (mp) REVERT: A 578 ARG cc_start: 0.7576 (mtm180) cc_final: 0.7372 (ptt90) REVERT: A 691 ASP cc_start: 0.8069 (p0) cc_final: 0.7702 (p0) REVERT: B 344 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8928 (mp) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.2490 time to fit residues: 25.2566 Evaluate side-chains 59 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 62.2267 > 50: distance: 35 - 108: 6.699 distance: 48 - 112: 14.022 distance: 51 - 109: 10.455 distance: 75 - 79: 28.862 distance: 79 - 80: 33.803 distance: 80 - 81: 30.009 distance: 80 - 83: 8.977 distance: 81 - 82: 35.830 distance: 81 - 87: 27.501 distance: 83 - 84: 4.327 distance: 84 - 85: 16.859 distance: 84 - 86: 8.679 distance: 87 - 88: 9.536 distance: 88 - 89: 15.455 distance: 88 - 91: 13.344 distance: 89 - 90: 19.461 distance: 89 - 95: 16.913 distance: 91 - 92: 8.468 distance: 92 - 93: 9.547 distance: 92 - 94: 14.422 distance: 95 - 96: 8.510 distance: 96 - 97: 24.206 distance: 96 - 99: 14.565 distance: 97 - 98: 47.981 distance: 97 - 103: 9.201 distance: 99 - 100: 19.379 distance: 100 - 101: 17.290 distance: 101 - 102: 5.521 distance: 103 - 104: 15.007 distance: 104 - 105: 11.124 distance: 104 - 107: 9.741 distance: 105 - 106: 9.420 distance: 105 - 109: 25.214 distance: 107 - 108: 11.801 distance: 109 - 110: 13.075 distance: 110 - 111: 8.864 distance: 111 - 112: 11.934 distance: 111 - 116: 11.981 distance: 113 - 114: 20.511 distance: 113 - 115: 18.966 distance: 116 - 117: 11.960 distance: 116 - 122: 6.648 distance: 117 - 118: 14.365 distance: 117 - 120: 9.591 distance: 118 - 119: 27.128 distance: 118 - 123: 14.302 distance: 120 - 121: 7.803 distance: 121 - 122: 14.679 distance: 123 - 124: 22.189 distance: 124 - 125: 19.997 distance: 124 - 127: 10.193 distance: 125 - 126: 33.660 distance: 125 - 129: 26.615 distance: 127 - 128: 17.024 distance: 129 - 130: 18.775 distance: 130 - 131: 31.599 distance: 130 - 133: 9.233 distance: 131 - 132: 39.424 distance: 131 - 137: 34.280 distance: 133 - 134: 16.600 distance: 134 - 135: 39.509 distance: 134 - 136: 44.551 distance: 137 - 138: 44.990 distance: 138 - 139: 4.040 distance: 139 - 140: 22.997 distance: 139 - 141: 15.915 distance: 141 - 142: 36.199 distance: 141 - 147: 24.431 distance: 142 - 143: 16.594 distance: 142 - 145: 26.990 distance: 143 - 144: 23.770 distance: 143 - 148: 6.690 distance: 145 - 146: 17.449 distance: 146 - 147: 37.580