Starting phenix.real_space_refine on Fri Feb 6 16:47:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vh3_43233/02_2026/8vh3_43233_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vh3_43233/02_2026/8vh3_43233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vh3_43233/02_2026/8vh3_43233_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vh3_43233/02_2026/8vh3_43233_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vh3_43233/02_2026/8vh3_43233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vh3_43233/02_2026/8vh3_43233.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.300 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: 5 Type Number sf(0) Gaussians S 108 5.16 5 C 8550 2.51 5 N 2367 2.21 5 O 2547 1.98 5 H 13440 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27012 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 7105 Classifications: {'peptide': 452} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 1 Chain: "Z" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1899 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 7105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 7105 Classifications: {'peptide': 452} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1899 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "I" Number of atoms: 7105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 7105 Classifications: {'peptide': 452} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 1 Chain: "J" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1899 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Time building chain proxies: 4.60, per 1000 atoms: 0.17 Number of scatterers: 27012 At special positions: 0 Unit cell: (129.6, 131.76, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 O 2547 8.00 N 2367 7.00 C 8550 6.00 H 13440 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 465 " distance=2.04 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS Z 605 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 457 " - pdb=" SG CYS E 465 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 457 " - pdb=" SG CYS I 465 " distance=2.03 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " 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: 2.15 Conformation dependent library (CDL) restraints added in 789.1 milliseconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 26 sheets defined 26.9% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 68 through 74 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.840A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.642A pdb=" N SER A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.917A pdb=" N ASP A 475 " --> pdb=" O ASN A 472 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 478 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 534 Processing helix chain 'Z' and resid 536 through 542 removed outlier: 3.953A pdb=" N GLN Z 540 " --> pdb=" O THR Z 536 " (cutoff:3.500A) Processing helix chain 'Z' and resid 572 through 593 removed outlier: 3.576A pdb=" N ALA Z 578 " --> pdb=" O LYS Z 574 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP Z 589 " --> pdb=" O ARG Z 585 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU Z 593 " --> pdb=" O ASP Z 589 " (cutoff:3.500A) Processing helix chain 'Z' and resid 594 through 597 Processing helix chain 'Z' and resid 627 through 636 Processing helix chain 'Z' and resid 638 through 661 removed outlier: 4.319A pdb=" N GLY Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) Processing helix chain 'Z' and resid 662 through 664 No H-bonds generated for 'chain 'Z' and resid 662 through 664' Processing helix chain 'E' and resid 68 through 74 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.858A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 205 through 209 removed outlier: 3.635A pdb=" N SER E 209 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.864A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 473 through 480 removed outlier: 3.821A pdb=" N SER E 479 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.160A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 595 removed outlier: 3.736A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU F 593 " --> pdb=" O ASP F 589 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.563A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'I' and resid 68 through 73 Processing helix chain 'I' and resid 94 through 98 Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.884A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP I 112 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 137 through 139 No H-bonds generated for 'chain 'I' and resid 137 through 139' Processing helix chain 'I' and resid 205 through 209 removed outlier: 3.626A pdb=" N SER I 209 " --> pdb=" O PRO I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.788A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 473 through 477 Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.984A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 595 removed outlier: 3.628A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU J 593 " --> pdb=" O ASP J 589 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY J 594 " --> pdb=" O GLN J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 661 removed outlier: 4.249A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU J 645 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 662 through 664 No H-bonds generated for 'chain 'J' and resid 662 through 664' Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 5.316A pdb=" N VAL Z 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 38 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR Z 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR A 40 " --> pdb=" O CYS Z 604 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N CYS Z 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.983A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 244 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.753A pdb=" N CYS A 218 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.520A pdb=" N SER A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA A 134 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N GLY A 144 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N THR A 132 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N LYS A 146 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N ASN A 130 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.169A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.217A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.005A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 10.039A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.589A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.421A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 308 removed outlier: 7.001A pdb=" N ASN A 301 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'E' and resid 492 through 497 removed outlier: 5.360A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.000A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 244 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.628A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS E 216 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 169 through 177 removed outlier: 4.984A pdb=" N ALA E 134 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N GLY E 144 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR E 132 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N LYS E 146 " --> pdb=" O ASN E 130 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ASN E 130 " --> pdb=" O LYS E 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.728A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.509A pdb=" N LEU E 288 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 301 through 308 removed outlier: 6.836A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 394 through 395 Processing sheet with id=AB9, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC1, first strand: chain 'I' and resid 492 through 497 removed outlier: 5.355A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.008A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR I 244 " --> pdb=" O MET I 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 169 through 177 removed outlier: 5.147A pdb=" N ALA I 134 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N GLY I 144 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N THR I 132 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N LYS I 146 " --> pdb=" O ASN I 130 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ASN I 130 " --> pdb=" O LYS I 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 271 through 273 removed outlier: 4.153A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.137A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.520A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 301 through 308 removed outlier: 6.810A pdb=" N ASN I 301 " --> pdb=" O VAL I 322 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 394 through 395 removed outlier: 6.491A pdb=" N THR I 359 " --> pdb=" O PHE I 466 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 423 through 424 455 hydrogen bonds defined for protein. 1137 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: 6.42 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13440 1.04 - 1.23: 674 1.23 - 1.43: 5076 1.43 - 1.63: 7954 1.63 - 1.83: 144 Bond restraints: 27288 Sorted by residual: bond pdb=" C ASP E 78 " pdb=" N PRO E 79 " ideal model delta sigma weight residual 1.333 1.322 0.011 1.01e-02 9.80e+03 1.25e+00 bond pdb=" CA ILE E 423 " pdb=" CB ILE E 423 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.97e-01 bond pdb=" N SER F 528 " pdb=" CA SER F 528 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.98e-01 bond pdb=" CA ASP I 78 " pdb=" C ASP I 78 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.82e-01 bond pdb=" C MET F 626 " pdb=" N THR F 627 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.53e-01 ... (remaining 27283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 47963 1.40 - 2.81: 1242 2.81 - 4.21: 90 4.21 - 5.61: 7 5.61 - 7.02: 3 Bond angle restraints: 49305 Sorted by residual: angle pdb=" N SER J 620 " pdb=" CA SER J 620 " pdb=" C SER J 620 " ideal model delta sigma weight residual 114.04 107.08 6.96 1.24e+00 6.50e-01 3.15e+01 angle pdb=" N SER Z 620 " pdb=" CA SER Z 620 " pdb=" C SER Z 620 " ideal model delta sigma weight residual 112.72 106.64 6.08 1.28e+00 6.10e-01 2.26e+01 angle pdb=" C MET F 626 " pdb=" N THR F 627 " pdb=" CA THR F 627 " ideal model delta sigma weight residual 121.70 128.72 -7.02 1.80e+00 3.09e-01 1.52e+01 angle pdb=" C CYS A 74 " pdb=" N VAL A 75 " pdb=" CA VAL A 75 " ideal model delta sigma weight residual 120.33 123.26 -2.93 8.00e-01 1.56e+00 1.35e+01 angle pdb=" N ILE J 622 " pdb=" CA ILE J 622 " pdb=" C ILE J 622 " ideal model delta sigma weight residual 112.90 109.81 3.09 9.60e-01 1.09e+00 1.04e+01 ... (remaining 49300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11724 17.93 - 35.86: 897 35.86 - 53.79: 207 53.79 - 71.72: 57 71.72 - 89.65: 21 Dihedral angle restraints: 12906 sinusoidal: 7098 harmonic: 5808 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -136.44 50.44 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -136.01 50.01 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA ASN F 625 " pdb=" C ASN F 625 " pdb=" N MET F 626 " pdb=" CA MET F 626 " ideal model delta harmonic sigma weight residual -180.00 -150.87 -29.13 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 12903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1308 0.031 - 0.063: 535 0.063 - 0.094: 129 0.094 - 0.125: 132 0.125 - 0.156: 17 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CA ILE I 213 " pdb=" N ILE I 213 " pdb=" C ILE I 213 " pdb=" CB ILE I 213 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE E 213 " pdb=" N ILE E 213 " pdb=" C ILE E 213 " pdb=" CB ILE E 213 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 2118 not shown) Planarity restraints: 4035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 211 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 212 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 211 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO I 212 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO I 212 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 212 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 211 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO E 212 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 212 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 212 " 0.028 5.00e-02 4.00e+02 ... (remaining 4032 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 13699 2.43 - 2.97: 60214 2.97 - 3.52: 63921 3.52 - 4.06: 87381 4.06 - 4.60: 128457 Nonbonded interactions: 353672 Sorted by model distance: nonbonded pdb=" HA MET A 104 " pdb=" HH TYR A 217 " model vdw 1.891 2.270 nonbonded pdb=" H SER Z 636 " pdb=" HG SER Z 636 " model vdw 1.904 2.100 nonbonded pdb=" HE3 TRP J 571 " pdb=" HB3 LYS J 574 " model vdw 1.914 2.270 nonbonded pdb=" H SER J 620 " pdb=" H GLU J 621 " model vdw 1.916 2.100 nonbonded pdb=" HD3 ARG I 192 " pdb="HH11 ARG I 192 " model vdw 1.921 2.270 ... (remaining 353667 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.930 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13884 Z= 0.144 Angle : 0.598 7.017 18861 Z= 0.361 Chirality : 0.043 0.156 2121 Planarity : 0.004 0.053 2397 Dihedral : 13.412 89.649 5094 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.20), residues: 1692 helix: -0.24 (0.29), residues: 357 sheet: -1.60 (0.26), residues: 360 loop : -1.09 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 273 TYR 0.007 0.001 TYR E 61 PHE 0.009 0.001 PHE A 376 TRP 0.009 0.001 TRP I 338 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00291 (13848) covalent geometry : angle 0.59585 (18789) SS BOND : bond 0.00261 ( 36) SS BOND : angle 0.98908 ( 72) hydrogen bonds : bond 0.22557 ( 443) hydrogen bonds : angle 7.70788 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8715 (m-30) cc_final: 0.8369 (m-30) REVERT: A 412 ARG cc_start: 0.6791 (mtp85) cc_final: 0.6480 (ttp-170) REVERT: A 426 MET cc_start: 0.5374 (mmm) cc_final: 0.4670 (ptt) REVERT: A 480 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7277 (mt-10) REVERT: Z 585 ARG cc_start: 0.7333 (mtt-85) cc_final: 0.7080 (ttp80) REVERT: E 82 GLN cc_start: 0.6803 (mm-40) cc_final: 0.6058 (pp30) REVERT: E 393 ARG cc_start: 0.5940 (mmt180) cc_final: 0.5550 (mmt180) REVERT: E 412 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6569 (ttp-170) REVERT: E 426 MET cc_start: 0.5484 (mmm) cc_final: 0.4759 (ptt) REVERT: E 479 SER cc_start: 0.8822 (m) cc_final: 0.8520 (t) REVERT: E 480 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7048 (mt-10) REVERT: F 626 MET cc_start: 0.7403 (tpt) cc_final: 0.7143 (tpt) REVERT: F 634 GLU cc_start: 0.7444 (tp30) cc_final: 0.7148 (tt0) REVERT: I 100 MET cc_start: 0.8582 (mtp) cc_final: 0.8342 (mtm) REVERT: I 318 TYR cc_start: 0.7726 (m-80) cc_final: 0.7442 (m-80) REVERT: I 377 ASN cc_start: 0.8580 (p0) cc_final: 0.8076 (p0) REVERT: I 393 ARG cc_start: 0.6115 (mmt180) cc_final: 0.5910 (mmt180) REVERT: I 426 MET cc_start: 0.5663 (mmm) cc_final: 0.4968 (ptt) REVERT: J 571 TRP cc_start: 0.5037 (t60) cc_final: 0.4682 (t60) REVERT: J 585 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.7168 (ttp80) REVERT: J 616 ASN cc_start: 0.4497 (t0) cc_final: 0.4029 (p0) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3568 time to fit residues: 136.0449 Evaluate side-chains 160 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Z 540 GLN Z 607 ASN E 300 ASN E 422 GLN I 94 ASN I 422 GLN I 476 ASN J 607 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135345 restraints weight = 465461.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.139165 restraints weight = 282183.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.138003 restraints weight = 218153.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138629 restraints weight = 227831.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138554 restraints weight = 213035.854| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13884 Z= 0.150 Angle : 0.547 7.209 18861 Z= 0.301 Chirality : 0.044 0.146 2121 Planarity : 0.004 0.065 2397 Dihedral : 5.647 26.573 1836 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.33 % Allowed : 6.56 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.20), residues: 1692 helix: -0.06 (0.29), residues: 348 sheet: -1.47 (0.28), residues: 324 loop : -1.20 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 327 TYR 0.008 0.001 TYR E 61 PHE 0.011 0.001 PHE I 376 TRP 0.011 0.001 TRP F 631 HIS 0.003 0.001 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00348 (13848) covalent geometry : angle 0.54542 (18789) SS BOND : bond 0.00325 ( 36) SS BOND : angle 0.81180 ( 72) hydrogen bonds : bond 0.05295 ( 443) hydrogen bonds : angle 5.58986 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7285 (tp40) cc_final: 0.5447 (pp30) REVERT: A 88 ASN cc_start: 0.7332 (t0) cc_final: 0.7094 (t0) REVERT: A 180 ASP cc_start: 0.8669 (m-30) cc_final: 0.8353 (m-30) REVERT: A 426 MET cc_start: 0.5424 (mmm) cc_final: 0.4627 (ptt) REVERT: A 480 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7204 (mt-10) REVERT: A 502 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8041 (mtt180) REVERT: E 393 ARG cc_start: 0.5967 (mmt180) cc_final: 0.5534 (mmt180) REVERT: E 412 ARG cc_start: 0.7227 (mtp85) cc_final: 0.6560 (ttp-170) REVERT: E 426 MET cc_start: 0.5506 (mmm) cc_final: 0.4707 (ptt) REVERT: E 479 SER cc_start: 0.8893 (m) cc_final: 0.8586 (t) REVERT: E 480 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6985 (mt-10) REVERT: F 626 MET cc_start: 0.7248 (tpt) cc_final: 0.6972 (tpt) REVERT: I 88 ASN cc_start: 0.7356 (t0) cc_final: 0.7047 (t0) REVERT: I 326 ILE cc_start: 0.8317 (pt) cc_final: 0.8112 (mt) REVERT: I 393 ARG cc_start: 0.6105 (mmt180) cc_final: 0.5831 (mmt180) REVERT: I 412 ARG cc_start: 0.7246 (mtp85) cc_final: 0.6490 (ttp-170) REVERT: I 426 MET cc_start: 0.5979 (mmm) cc_final: 0.5037 (ptt) REVERT: J 585 ARG cc_start: 0.7581 (mtt-85) cc_final: 0.7184 (ttp80) REVERT: J 616 ASN cc_start: 0.4473 (t0) cc_final: 0.3862 (p0) outliers start: 5 outliers final: 2 residues processed: 168 average time/residue: 0.3015 time to fit residues: 70.7889 Evaluate side-chains 144 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain J residue 607 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN Z 607 ASN E 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.133040 restraints weight = 475629.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.138205 restraints weight = 276928.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.135890 restraints weight = 209244.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.136379 restraints weight = 218879.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.136179 restraints weight = 210147.085| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13884 Z= 0.173 Angle : 0.545 7.050 18861 Z= 0.301 Chirality : 0.044 0.146 2121 Planarity : 0.004 0.062 2397 Dihedral : 5.632 25.961 1836 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.79 % Allowed : 7.22 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.20), residues: 1692 helix: 0.10 (0.30), residues: 339 sheet: -1.71 (0.30), residues: 273 loop : -1.31 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.009 0.001 TYR E 61 PHE 0.012 0.001 PHE I 376 TRP 0.015 0.001 TRP J 571 HIS 0.005 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00408 (13848) covalent geometry : angle 0.54402 (18789) SS BOND : bond 0.00313 ( 36) SS BOND : angle 0.67967 ( 72) hydrogen bonds : bond 0.04728 ( 443) hydrogen bonds : angle 5.25833 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8711 (m-30) cc_final: 0.8386 (m-30) REVERT: A 426 MET cc_start: 0.5454 (mmm) cc_final: 0.4449 (ptt) REVERT: A 480 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7303 (mt-10) REVERT: Z 530 MET cc_start: 0.8067 (mtp) cc_final: 0.7642 (mtp) REVERT: E 82 GLN cc_start: 0.7485 (tp40) cc_final: 0.5124 (pp30) REVERT: E 393 ARG cc_start: 0.6141 (mmt180) cc_final: 0.5627 (mtt-85) REVERT: E 412 ARG cc_start: 0.7287 (mtp85) cc_final: 0.6525 (ttp-170) REVERT: E 426 MET cc_start: 0.5773 (mmm) cc_final: 0.4726 (ptt) REVERT: E 480 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6879 (mt-10) REVERT: F 626 MET cc_start: 0.7140 (tpt) cc_final: 0.6891 (tpt) REVERT: I 88 ASN cc_start: 0.7356 (t0) cc_final: 0.7046 (t0) REVERT: I 393 ARG cc_start: 0.6180 (mmt180) cc_final: 0.5735 (mtt-85) REVERT: I 412 ARG cc_start: 0.7409 (mtp85) cc_final: 0.6561 (ttp-170) REVERT: I 426 MET cc_start: 0.5973 (mmm) cc_final: 0.5019 (ptt) REVERT: J 585 ARG cc_start: 0.7517 (mtt-85) cc_final: 0.7193 (ttp80) REVERT: J 616 ASN cc_start: 0.4391 (t0) cc_final: 0.3799 (p0) outliers start: 12 outliers final: 6 residues processed: 147 average time/residue: 0.2952 time to fit residues: 61.5968 Evaluate side-chains 139 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain Z residue 641 ILE Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain I residue 131 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 607 ASN F 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133286 restraints weight = 480480.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.137930 restraints weight = 286543.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.136315 restraints weight = 220004.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.136430 restraints weight = 221308.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.136330 restraints weight = 219566.867| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13884 Z= 0.160 Angle : 0.525 6.647 18861 Z= 0.288 Chirality : 0.044 0.144 2121 Planarity : 0.004 0.062 2397 Dihedral : 5.499 27.005 1836 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.05 % Allowed : 8.40 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.20), residues: 1692 helix: 0.24 (0.30), residues: 339 sheet: -1.78 (0.30), residues: 273 loop : -1.32 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.009 0.001 TYR E 482 PHE 0.011 0.001 PHE E 93 TRP 0.012 0.001 TRP J 571 HIS 0.006 0.002 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00381 (13848) covalent geometry : angle 0.52453 (18789) SS BOND : bond 0.00318 ( 36) SS BOND : angle 0.63795 ( 72) hydrogen bonds : bond 0.04054 ( 443) hydrogen bonds : angle 4.99427 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.7401 (t0) cc_final: 0.7143 (t0) REVERT: A 180 ASP cc_start: 0.8761 (m-30) cc_final: 0.8480 (m-30) REVERT: A 426 MET cc_start: 0.5809 (mmm) cc_final: 0.4772 (ptt) REVERT: A 480 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7369 (mt-10) REVERT: Z 657 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7515 (mm-30) REVERT: E 82 GLN cc_start: 0.7530 (tp40) cc_final: 0.5221 (pp30) REVERT: E 267 GLU cc_start: 0.7003 (mp0) cc_final: 0.6619 (mp0) REVERT: E 412 ARG cc_start: 0.7552 (mtp85) cc_final: 0.6536 (ttp-170) REVERT: E 426 MET cc_start: 0.5886 (mmm) cc_final: 0.4749 (ptt) REVERT: E 480 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6985 (mt-10) REVERT: E 502 ARG cc_start: 0.8295 (mtt180) cc_final: 0.8043 (mtt180) REVERT: I 88 ASN cc_start: 0.7691 (t0) cc_final: 0.7331 (t0) REVERT: I 393 ARG cc_start: 0.5996 (mmt180) cc_final: 0.5753 (mtt-85) REVERT: I 412 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6600 (ttp-170) REVERT: I 426 MET cc_start: 0.6022 (mmm) cc_final: 0.4875 (ptt) REVERT: J 585 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.7206 (ttp80) REVERT: J 616 ASN cc_start: 0.4384 (t0) cc_final: 0.3868 (p0) outliers start: 16 outliers final: 16 residues processed: 161 average time/residue: 0.2962 time to fit residues: 67.9954 Evaluate side-chains 155 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain Z residue 607 ASN Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 327 ARG Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 499 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.161421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134581 restraints weight = 469076.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.139501 restraints weight = 275370.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.137217 restraints weight = 209589.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137749 restraints weight = 220417.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.137664 restraints weight = 209356.383| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13884 Z= 0.120 Angle : 0.499 6.467 18861 Z= 0.273 Chirality : 0.043 0.142 2121 Planarity : 0.004 0.063 2397 Dihedral : 5.321 27.268 1836 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.05 % Allowed : 9.91 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.20), residues: 1692 helix: 0.38 (0.30), residues: 339 sheet: -1.72 (0.30), residues: 273 loop : -1.27 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.008 0.001 TYR E 61 PHE 0.008 0.001 PHE I 376 TRP 0.009 0.001 TRP I 338 HIS 0.004 0.001 HIS I 287 Details of bonding type rmsd covalent geometry : bond 0.00280 (13848) covalent geometry : angle 0.49828 (18789) SS BOND : bond 0.00365 ( 36) SS BOND : angle 0.55405 ( 72) hydrogen bonds : bond 0.03719 ( 443) hydrogen bonds : angle 4.82876 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.7397 (t0) cc_final: 0.7118 (t0) REVERT: A 426 MET cc_start: 0.5738 (mmm) cc_final: 0.4690 (ptt) REVERT: A 480 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7369 (mt-10) REVERT: Z 530 MET cc_start: 0.8115 (mtp) cc_final: 0.7780 (mtp) REVERT: E 267 GLU cc_start: 0.7130 (mp0) cc_final: 0.6856 (mp0) REVERT: E 412 ARG cc_start: 0.7540 (mtp85) cc_final: 0.6524 (ttp-170) REVERT: E 426 MET cc_start: 0.5820 (mmm) cc_final: 0.4682 (ptt) REVERT: E 480 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6845 (mt-10) REVERT: F 657 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7596 (mm-30) REVERT: I 88 ASN cc_start: 0.7511 (t0) cc_final: 0.7224 (t0) REVERT: I 393 ARG cc_start: 0.6072 (mmt180) cc_final: 0.5785 (mtt-85) REVERT: I 412 ARG cc_start: 0.7564 (mtp85) cc_final: 0.6628 (ttp-170) REVERT: I 426 MET cc_start: 0.5949 (mmm) cc_final: 0.4852 (ptt) REVERT: J 585 ARG cc_start: 0.7438 (mtt-85) cc_final: 0.7138 (ttp80) REVERT: J 616 ASN cc_start: 0.4404 (t0) cc_final: 0.3855 (p0) outliers start: 16 outliers final: 14 residues processed: 153 average time/residue: 0.2740 time to fit residues: 61.0456 Evaluate side-chains 148 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 327 ARG Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 499 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 0 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 607 ASN F 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130283 restraints weight = 476075.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134050 restraints weight = 288130.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.132865 restraints weight = 225860.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133068 restraints weight = 235180.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.132969 restraints weight = 228261.865| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13884 Z= 0.213 Angle : 0.569 6.664 18861 Z= 0.313 Chirality : 0.045 0.150 2121 Planarity : 0.004 0.056 2397 Dihedral : 5.570 26.725 1836 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.64 % Allowed : 10.43 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.20), residues: 1692 helix: 0.30 (0.30), residues: 339 sheet: -2.05 (0.28), residues: 309 loop : -1.41 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 617 TYR 0.013 0.002 TYR A 435 PHE 0.015 0.002 PHE E 93 TRP 0.009 0.001 TRP I 338 HIS 0.008 0.002 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00507 (13848) covalent geometry : angle 0.56799 (18789) SS BOND : bond 0.00324 ( 36) SS BOND : angle 0.77407 ( 72) hydrogen bonds : bond 0.04190 ( 443) hydrogen bonds : angle 4.96141 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.7433 (t0) cc_final: 0.7193 (t0) REVERT: A 180 ASP cc_start: 0.8898 (m-30) cc_final: 0.8646 (m-30) REVERT: A 412 ARG cc_start: 0.7241 (mtp85) cc_final: 0.6442 (ttp-170) REVERT: A 426 MET cc_start: 0.5618 (mmm) cc_final: 0.4456 (ptt) REVERT: A 480 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7359 (mt-10) REVERT: E 267 GLU cc_start: 0.7146 (mp0) cc_final: 0.6831 (mp0) REVERT: E 412 ARG cc_start: 0.7632 (mtp85) cc_final: 0.6479 (ttp-170) REVERT: E 426 MET cc_start: 0.6038 (mmm) cc_final: 0.4701 (ptt) REVERT: E 480 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7014 (mt-10) REVERT: F 571 TRP cc_start: 0.5336 (OUTLIER) cc_final: 0.3078 (m100) REVERT: I 88 ASN cc_start: 0.7909 (t0) cc_final: 0.7463 (t0) REVERT: I 236 THR cc_start: 0.8116 (t) cc_final: 0.7810 (p) REVERT: I 393 ARG cc_start: 0.5994 (mmt180) cc_final: 0.5705 (mtt-85) REVERT: I 412 ARG cc_start: 0.7544 (mtp85) cc_final: 0.6592 (ttp-170) REVERT: I 426 MET cc_start: 0.6067 (mmm) cc_final: 0.4996 (ptt) REVERT: I 477 TRP cc_start: 0.8322 (m-90) cc_final: 0.7765 (m-10) REVERT: J 616 ASN cc_start: 0.4056 (t0) cc_final: 0.3824 (p0) REVERT: J 638 TYR cc_start: 0.6031 (m-80) cc_final: 0.5776 (m-80) outliers start: 25 outliers final: 22 residues processed: 159 average time/residue: 0.3131 time to fit residues: 70.4089 Evaluate side-chains 161 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 276 ASN Chi-restraints excluded: chain I residue 327 ARG Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 499 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 36 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.158142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131475 restraints weight = 473298.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134683 restraints weight = 289434.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.134297 restraints weight = 222567.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134592 restraints weight = 225925.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134710 restraints weight = 215030.816| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13884 Z= 0.150 Angle : 0.524 6.483 18861 Z= 0.287 Chirality : 0.043 0.145 2121 Planarity : 0.004 0.057 2397 Dihedral : 5.408 27.880 1836 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.31 % Allowed : 11.15 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1692 helix: 0.40 (0.30), residues: 339 sheet: -1.96 (0.30), residues: 273 loop : -1.43 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.009 0.001 TYR E 61 PHE 0.011 0.001 PHE E 93 TRP 0.010 0.001 TRP A 338 HIS 0.006 0.002 HIS I 287 Details of bonding type rmsd covalent geometry : bond 0.00357 (13848) covalent geometry : angle 0.52249 (18789) SS BOND : bond 0.00362 ( 36) SS BOND : angle 0.88891 ( 72) hydrogen bonds : bond 0.03777 ( 443) hydrogen bonds : angle 4.84771 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASN cc_start: 0.7565 (t0) cc_final: 0.7360 (t0) REVERT: A 180 ASP cc_start: 0.8865 (m-30) cc_final: 0.8586 (m-30) REVERT: A 426 MET cc_start: 0.5830 (mmm) cc_final: 0.4690 (ptt) REVERT: A 480 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7457 (mt-10) REVERT: Z 657 GLU cc_start: 0.7828 (mm-30) cc_final: 0.6070 (tm-30) REVERT: E 267 GLU cc_start: 0.7187 (mp0) cc_final: 0.6637 (mt-10) REVERT: E 426 MET cc_start: 0.6123 (mmm) cc_final: 0.4758 (ptt) REVERT: E 480 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6906 (mt-10) REVERT: F 571 TRP cc_start: 0.5321 (OUTLIER) cc_final: 0.3073 (m100) REVERT: I 88 ASN cc_start: 0.7602 (t0) cc_final: 0.7280 (t0) REVERT: I 393 ARG cc_start: 0.6096 (mmt180) cc_final: 0.5812 (mtt-85) REVERT: I 412 ARG cc_start: 0.7579 (mtp85) cc_final: 0.6681 (ttp-170) REVERT: I 426 MET cc_start: 0.5889 (mmm) cc_final: 0.4763 (ptt) REVERT: J 616 ASN cc_start: 0.4292 (t0) cc_final: 0.4013 (p0) REVERT: J 638 TYR cc_start: 0.5919 (m-80) cc_final: 0.5633 (m-80) outliers start: 20 outliers final: 17 residues processed: 146 average time/residue: 0.2843 time to fit residues: 60.4629 Evaluate side-chains 148 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 327 ARG Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 499 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.178402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.155458 restraints weight = 426433.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.159013 restraints weight = 244481.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158270 restraints weight = 192062.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.158270 restraints weight = 197747.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.158216 restraints weight = 194003.938| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13884 Z= 0.122 Angle : 0.494 6.465 18861 Z= 0.268 Chirality : 0.043 0.144 2121 Planarity : 0.004 0.057 2397 Dihedral : 5.196 27.786 1836 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.12 % Allowed : 11.42 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1692 helix: 0.55 (0.30), residues: 339 sheet: -1.51 (0.30), residues: 279 loop : -1.35 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 393 TYR 0.009 0.001 TYR A 318 PHE 0.009 0.001 PHE E 93 TRP 0.010 0.001 TRP E 338 HIS 0.006 0.001 HIS I 287 Details of bonding type rmsd covalent geometry : bond 0.00291 (13848) covalent geometry : angle 0.49280 (18789) SS BOND : bond 0.00273 ( 36) SS BOND : angle 0.70030 ( 72) hydrogen bonds : bond 0.03473 ( 443) hydrogen bonds : angle 4.67979 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.5836 (mmm) cc_final: 0.4761 (ptt) REVERT: A 480 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7332 (mt-10) REVERT: E 72 HIS cc_start: 0.3903 (t-170) cc_final: 0.3674 (t-170) REVERT: E 267 GLU cc_start: 0.7211 (mp0) cc_final: 0.6631 (mt-10) REVERT: E 426 MET cc_start: 0.5908 (mmm) cc_final: 0.4607 (ptt) REVERT: E 480 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6871 (mt-10) REVERT: F 571 TRP cc_start: 0.5294 (OUTLIER) cc_final: 0.3073 (m100) REVERT: I 88 ASN cc_start: 0.7605 (t0) cc_final: 0.7268 (t0) REVERT: I 393 ARG cc_start: 0.6016 (mmt180) cc_final: 0.5715 (mtt-85) REVERT: I 412 ARG cc_start: 0.7550 (mtp85) cc_final: 0.6663 (ttp-170) REVERT: I 426 MET cc_start: 0.5950 (mmm) cc_final: 0.4887 (ptt) REVERT: I 477 TRP cc_start: 0.8340 (m-90) cc_final: 0.7858 (m-10) REVERT: J 616 ASN cc_start: 0.4220 (t0) cc_final: 0.4020 (p0) REVERT: J 638 TYR cc_start: 0.5859 (m-80) cc_final: 0.5549 (m-80) outliers start: 17 outliers final: 16 residues processed: 148 average time/residue: 0.2723 time to fit residues: 59.2876 Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 499 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 152 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.179249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.156189 restraints weight = 426222.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.160731 restraints weight = 248318.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.159444 restraints weight = 188073.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.159191 restraints weight = 193771.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.159287 restraints weight = 194545.088| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13884 Z= 0.111 Angle : 0.483 6.387 18861 Z= 0.262 Chirality : 0.043 0.141 2121 Planarity : 0.004 0.058 2397 Dihedral : 5.052 27.715 1836 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.12 % Allowed : 11.61 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.20), residues: 1692 helix: 0.72 (0.31), residues: 339 sheet: -1.48 (0.30), residues: 282 loop : -1.31 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 502 TYR 0.007 0.001 TYR E 61 PHE 0.008 0.001 PHE E 93 TRP 0.010 0.001 TRP I 338 HIS 0.005 0.001 HIS I 287 Details of bonding type rmsd covalent geometry : bond 0.00265 (13848) covalent geometry : angle 0.48247 (18789) SS BOND : bond 0.00213 ( 36) SS BOND : angle 0.63689 ( 72) hydrogen bonds : bond 0.03302 ( 443) hydrogen bonds : angle 4.58273 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.5829 (mmm) cc_final: 0.4804 (ptt) REVERT: A 480 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7443 (mt-10) REVERT: A 502 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7608 (mtt180) REVERT: Z 616 ASN cc_start: 0.4017 (t0) cc_final: 0.3644 (p0) REVERT: E 145 MET cc_start: 0.8029 (mmm) cc_final: 0.7801 (mtp) REVERT: E 267 GLU cc_start: 0.7140 (mp0) cc_final: 0.6518 (mt-10) REVERT: E 426 MET cc_start: 0.6062 (mmm) cc_final: 0.4710 (ptt) REVERT: E 463 THR cc_start: 0.5082 (p) cc_final: 0.4781 (t) REVERT: E 480 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6849 (mt-10) REVERT: F 571 TRP cc_start: 0.5272 (OUTLIER) cc_final: 0.3054 (m100) REVERT: F 657 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7381 (mm-30) REVERT: I 88 ASN cc_start: 0.7663 (t0) cc_final: 0.7335 (t0) REVERT: I 393 ARG cc_start: 0.6062 (mmt180) cc_final: 0.5731 (mtt-85) REVERT: I 426 MET cc_start: 0.6013 (mmm) cc_final: 0.4918 (ptt) REVERT: I 477 TRP cc_start: 0.8352 (m-90) cc_final: 0.7915 (m-10) REVERT: J 616 ASN cc_start: 0.4359 (t0) cc_final: 0.3940 (p0) REVERT: J 638 TYR cc_start: 0.5768 (m-80) cc_final: 0.5503 (m-80) REVERT: J 657 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7687 (mm-30) outliers start: 17 outliers final: 14 residues processed: 155 average time/residue: 0.2674 time to fit residues: 61.3106 Evaluate side-chains 147 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 499 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 66 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.132591 restraints weight = 472256.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.137091 restraints weight = 270950.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.135094 restraints weight = 213412.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.135500 restraints weight = 222659.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.135331 restraints weight = 215290.116| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13884 Z= 0.121 Angle : 0.486 6.375 18861 Z= 0.264 Chirality : 0.043 0.142 2121 Planarity : 0.004 0.057 2397 Dihedral : 5.021 27.174 1836 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.31 % Allowed : 11.61 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.20), residues: 1692 helix: 0.76 (0.31), residues: 339 sheet: -1.58 (0.28), residues: 318 loop : -1.27 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 617 TYR 0.008 0.001 TYR E 61 PHE 0.008 0.001 PHE E 93 TRP 0.009 0.001 TRP A 338 HIS 0.008 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00289 (13848) covalent geometry : angle 0.48556 (18789) SS BOND : bond 0.00221 ( 36) SS BOND : angle 0.55729 ( 72) hydrogen bonds : bond 0.03303 ( 443) hydrogen bonds : angle 4.55928 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ARG cc_start: 0.7321 (mtp85) cc_final: 0.6488 (ttp-170) REVERT: A 426 MET cc_start: 0.5840 (mmm) cc_final: 0.4732 (ptt) REVERT: A 480 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7345 (mt-10) REVERT: Z 616 ASN cc_start: 0.4144 (t0) cc_final: 0.3664 (p0) REVERT: E 72 HIS cc_start: 0.3624 (OUTLIER) cc_final: 0.2725 (t-170) REVERT: E 145 MET cc_start: 0.8128 (mmm) cc_final: 0.7871 (mtp) REVERT: E 267 GLU cc_start: 0.7058 (mp0) cc_final: 0.6552 (mt-10) REVERT: E 426 MET cc_start: 0.5931 (mmm) cc_final: 0.4582 (ptt) REVERT: E 463 THR cc_start: 0.5140 (p) cc_final: 0.4816 (t) REVERT: E 480 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6856 (mt-10) REVERT: F 571 TRP cc_start: 0.5235 (OUTLIER) cc_final: 0.2995 (m100) REVERT: I 88 ASN cc_start: 0.7795 (t0) cc_final: 0.7483 (t0) REVERT: I 393 ARG cc_start: 0.5925 (mmt180) cc_final: 0.5610 (mtt-85) REVERT: I 426 MET cc_start: 0.6068 (mmm) cc_final: 0.4878 (ptt) REVERT: I 477 TRP cc_start: 0.8352 (m-90) cc_final: 0.7937 (m-10) REVERT: J 616 ASN cc_start: 0.4322 (t0) cc_final: 0.3983 (p0) REVERT: J 638 TYR cc_start: 0.5920 (m-80) cc_final: 0.5645 (m-80) outliers start: 20 outliers final: 17 residues processed: 148 average time/residue: 0.3016 time to fit residues: 64.7837 Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 499 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 70 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 126 optimal weight: 0.0070 chunk 169 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.179277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.156369 restraints weight = 425954.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.160793 restraints weight = 242922.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.159434 restraints weight = 189514.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.159719 restraints weight = 193490.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.159529 restraints weight = 183516.732| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13884 Z= 0.115 Angle : 0.482 6.262 18861 Z= 0.262 Chirality : 0.043 0.142 2121 Planarity : 0.004 0.057 2397 Dihedral : 4.984 27.165 1836 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.25 % Allowed : 11.68 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.20), residues: 1692 helix: 0.80 (0.31), residues: 339 sheet: -1.46 (0.27), residues: 354 loop : -1.20 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 617 TYR 0.008 0.001 TYR E 61 PHE 0.008 0.001 PHE E 93 TRP 0.010 0.001 TRP A 338 HIS 0.007 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00272 (13848) covalent geometry : angle 0.48196 (18789) SS BOND : bond 0.00240 ( 36) SS BOND : angle 0.57002 ( 72) hydrogen bonds : bond 0.03376 ( 443) hydrogen bonds : angle 4.54933 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.55 seconds wall clock time: 63 minutes 33.40 seconds (3813.40 seconds total)