Starting phenix.real_space_refine on Sun May 25 11:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vh3_43233/05_2025/8vh3_43233_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vh3_43233/05_2025/8vh3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vh3_43233/05_2025/8vh3_43233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vh3_43233/05_2025/8vh3_43233.map" model { file = "/net/cci-nas-00/data/ceres_data/8vh3_43233/05_2025/8vh3_43233_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vh3_43233/05_2025/8vh3_43233_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.06, per 1000 atoms: 0.48 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: 7.69 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.26 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: 10.46 Time building geometry restraints manager: 9.17 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: 0.04 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: 2.410 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: 0.490 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 57.980 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (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 TRP 0.009 0.001 TRP I 338 HIS 0.004 0.001 HIS A 249 PHE 0.009 0.001 PHE A 376 TYR 0.007 0.001 TYR E 61 ARG 0.002 0.000 ARG I 273 Details of bonding type rmsd hydrogen bonds : bond 0.22557 ( 443) hydrogen bonds : angle 7.70788 ( 1137) SS BOND : bond 0.00261 ( 36) SS BOND : angle 0.98908 ( 72) covalent geometry : bond 0.00291 (13848) covalent geometry : angle 0.59585 (18789) *********************** 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 : 1.975 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: 0.8367 (m-30) REVERT: A 412 ARG cc_start: 0.6791 (mtp85) cc_final: 0.6481 (ttp-170) REVERT: A 426 MET cc_start: 0.5374 (mmm) cc_final: 0.4666 (ptt) REVERT: A 480 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7278 (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: 0.6057 (pp30) REVERT: E 393 ARG cc_start: 0.5940 (mmt180) cc_final: 0.5553 (mmt180) REVERT: E 412 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6570 (ttp-170) REVERT: E 426 MET cc_start: 0.5484 (mmm) cc_final: 0.4764 (ptt) REVERT: E 479 SER cc_start: 0.8822 (m) cc_final: 0.8570 (t) REVERT: E 480 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7066 (mt-10) REVERT: F 626 MET cc_start: 0.7403 (tpt) cc_final: 0.7144 (tpt) REVERT: F 634 GLU cc_start: 0.7444 (tp30) cc_final: 0.7146 (tt0) REVERT: I 318 TYR cc_start: 0.7726 (m-80) cc_final: 0.7447 (m-80) REVERT: I 377 ASN cc_start: 0.8580 (p0) cc_final: 0.8078 (p0) REVERT: I 393 ARG cc_start: 0.6115 (mmt180) cc_final: 0.5909 (mmt180) REVERT: I 426 MET cc_start: 0.5663 (mmm) cc_final: 0.4958 (ptt) REVERT: J 571 TRP cc_start: 0.5037 (t60) cc_final: 0.4684 (t60) REVERT: J 585 ARG cc_start: 0.7480 (mtt-85) cc_final: 0.7166 (ttp80) REVERT: J 616 ASN cc_start: 0.4497 (t0) cc_final: 0.4032 (p0) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.7582 time to fit residues: 290.2325 Evaluate side-chains 163 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.186094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.163224 restraints weight = 414895.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.166777 restraints weight = 241214.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.166618 restraints weight = 188995.276| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2127 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= 0.146 Angle : 0.539 7.218 18861 Z= 0.299 Chirality : 0.043 0.145 2121 Planarity : 0.004 0.065 2397 Dihedral : 5.625 26.801 1836 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.33 % Allowed : 6.50 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.20), residues: 1692 helix: -0.05 (0.29), residues: 348 sheet: -1.49 (0.28), residues: 324 loop : -1.16 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 631 HIS 0.003 0.001 HIS I 249 PHE 0.010 0.001 PHE I 376 TYR 0.008 0.001 TYR E 61 ARG 0.003 0.000 ARG E 327 Details of bonding type rmsd hydrogen bonds : bond 0.05859 ( 443) hydrogen bonds : angle 5.68576 ( 1137) SS BOND : bond 0.00277 ( 36) SS BOND : angle 0.86702 ( 72) covalent geometry : bond 0.00333 (13848) covalent geometry : angle 0.53762 (18789) *********************** 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 : 2.342 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 82 GLN cc_start: 0.7077 (tp40) cc_final: 0.5249 (pp30) REVERT: A 88 ASN cc_start: 0.7290 (t0) cc_final: 0.7049 (t0) REVERT: A 426 MET cc_start: 0.5374 (mmm) cc_final: 0.4643 (ptt) REVERT: A 480 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7189 (mt-10) REVERT: E 393 ARG cc_start: 0.6029 (mmt180) cc_final: 0.5609 (mmt180) REVERT: E 412 ARG cc_start: 0.7195 (mtp85) cc_final: 0.6620 (ttp-170) REVERT: E 426 MET cc_start: 0.5481 (mmm) cc_final: 0.4736 (ptt) REVERT: E 479 SER cc_start: 0.8869 (m) cc_final: 0.8602 (t) REVERT: E 480 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7010 (mt-10) REVERT: F 626 MET cc_start: 0.7252 (tpt) cc_final: 0.6970 (tpt) REVERT: I 88 ASN cc_start: 0.7392 (t0) cc_final: 0.7083 (t0) REVERT: I 318 TYR cc_start: 0.7651 (m-80) cc_final: 0.7441 (m-80) REVERT: I 393 ARG cc_start: 0.6140 (mmt180) cc_final: 0.5876 (mmt180) REVERT: I 412 ARG cc_start: 0.7225 (mtp85) cc_final: 0.6530 (ttp-170) REVERT: I 426 MET cc_start: 0.5975 (mmm) cc_final: 0.5081 (ptt) REVERT: J 585 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.7183 (ttp80) REVERT: J 616 ASN cc_start: 0.4390 (t0) cc_final: 0.3837 (p0) outliers start: 5 outliers final: 2 residues processed: 168 average time/residue: 0.6330 time to fit residues: 150.0927 Evaluate side-chains 145 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.163378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.135254 restraints weight = 472859.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.139602 restraints weight = 278851.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.137934 restraints weight = 215937.853| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13884 Z= 0.133 Angle : 0.517 6.861 18861 Z= 0.284 Chirality : 0.043 0.143 2121 Planarity : 0.004 0.063 2397 Dihedral : 5.506 26.296 1836 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.59 % Allowed : 7.09 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1692 helix: 0.19 (0.30), residues: 339 sheet: -1.41 (0.28), residues: 324 loop : -1.20 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 571 HIS 0.005 0.001 HIS E 72 PHE 0.009 0.001 PHE I 376 TYR 0.008 0.001 TYR E 61 ARG 0.002 0.000 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 443) hydrogen bonds : angle 5.22386 ( 1137) SS BOND : bond 0.00272 ( 36) SS BOND : angle 0.61268 ( 72) covalent geometry : bond 0.00311 (13848) covalent geometry : angle 0.51658 (18789) *********************** 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 156 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 2.479 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 88 ASN cc_start: 0.7462 (t0) cc_final: 0.7256 (t0) REVERT: A 426 MET cc_start: 0.5309 (mmm) cc_final: 0.4378 (ptt) REVERT: A 480 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7237 (mt-10) REVERT: Z 530 MET cc_start: 0.8325 (mtp) cc_final: 0.7711 (mtp) REVERT: Z 641 ILE cc_start: 0.7744 (mp) cc_final: 0.7466 (tt) REVERT: Z 657 GLU cc_start: 0.7740 (mm-30) cc_final: 0.6897 (mm-30) REVERT: E 393 ARG cc_start: 0.6112 (mmt180) cc_final: 0.5628 (mmt180) REVERT: E 412 ARG cc_start: 0.7352 (mtp85) cc_final: 0.6568 (ttp-170) REVERT: E 426 MET cc_start: 0.5698 (mmm) cc_final: 0.4692 (ptt) REVERT: E 479 SER cc_start: 0.8933 (m) cc_final: 0.8694 (t) REVERT: E 480 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7001 (mt-10) REVERT: F 626 MET cc_start: 0.7115 (tpt) cc_final: 0.6900 (tpt) REVERT: I 82 GLN cc_start: 0.7233 (tp40) cc_final: 0.5250 (pp30) REVERT: I 88 ASN cc_start: 0.7281 (t0) cc_final: 0.6930 (t0) REVERT: I 393 ARG cc_start: 0.6182 (mmt180) cc_final: 0.5740 (mtt-85) REVERT: I 412 ARG cc_start: 0.7352 (mtp85) cc_final: 0.6540 (ttp-170) REVERT: I 426 MET cc_start: 0.5910 (mmm) cc_final: 0.4969 (ptt) REVERT: J 585 ARG cc_start: 0.7526 (mtt-85) cc_final: 0.7179 (ttp80) REVERT: J 616 ASN cc_start: 0.4430 (t0) cc_final: 0.3842 (p0) outliers start: 9 outliers final: 4 residues processed: 155 average time/residue: 0.6097 time to fit residues: 135.5138 Evaluate side-chains 139 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 327 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 607 ASN E 94 ASN F 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133769 restraints weight = 475441.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.138554 restraints weight = 285237.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.136567 restraints weight = 219166.035| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13884 Z= 0.149 Angle : 0.517 6.635 18861 Z= 0.284 Chirality : 0.043 0.145 2121 Planarity : 0.004 0.062 2397 Dihedral : 5.420 26.586 1836 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.12 % Allowed : 7.74 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.20), residues: 1692 helix: 0.30 (0.30), residues: 339 sheet: -1.68 (0.31), residues: 273 loop : -1.26 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 571 HIS 0.006 0.001 HIS A 287 PHE 0.010 0.001 PHE I 376 TYR 0.009 0.001 TYR E 482 ARG 0.003 0.000 ARG I 304 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 443) hydrogen bonds : angle 4.95425 ( 1137) SS BOND : bond 0.00272 ( 36) SS BOND : angle 0.62927 ( 72) covalent geometry : bond 0.00353 (13848) covalent geometry : angle 0.51615 (18789) *********************** 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 163 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 2.138 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 426 MET cc_start: 0.5736 (mmm) cc_final: 0.4732 (ptt) REVERT: A 480 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7332 (mt-10) REVERT: Z 530 MET cc_start: 0.8343 (mtp) cc_final: 0.7787 (mtp) REVERT: Z 641 ILE cc_start: 0.7968 (mp) cc_final: 0.7638 (tt) REVERT: Z 657 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7077 (mm-30) REVERT: E 82 GLN cc_start: 0.7302 (tp40) cc_final: 0.5086 (pp30) REVERT: E 267 GLU cc_start: 0.7040 (mp0) cc_final: 0.6676 (mp0) REVERT: E 412 ARG cc_start: 0.7555 (mtp85) cc_final: 0.6546 (ttp-170) REVERT: E 426 MET cc_start: 0.5834 (mmm) cc_final: 0.4727 (ptt) REVERT: E 480 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6955 (mt-10) REVERT: I 88 ASN cc_start: 0.7727 (t0) cc_final: 0.7304 (t0) REVERT: I 393 ARG cc_start: 0.5963 (mmt180) cc_final: 0.5508 (mtt-85) REVERT: I 412 ARG cc_start: 0.7448 (mtp85) cc_final: 0.6584 (ttp-170) REVERT: I 426 MET cc_start: 0.6090 (mmm) cc_final: 0.5028 (ptt) REVERT: J 585 ARG cc_start: 0.7651 (mtt-85) cc_final: 0.7226 (ttp80) REVERT: J 616 ASN cc_start: 0.4305 (t0) cc_final: 0.3784 (p0) outliers start: 17 outliers final: 14 residues processed: 159 average time/residue: 0.5951 time to fit residues: 136.5864 Evaluate side-chains 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 1.969 ------------------------------------------------------------------------------- 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 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 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 137 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 607 ASN E 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.158624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.131580 restraints weight = 476947.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134941 restraints weight = 283442.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.134054 restraints weight = 229622.458| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 13884 Z= 0.237 Angle : 0.581 6.795 18861 Z= 0.322 Chirality : 0.046 0.151 2121 Planarity : 0.005 0.060 2397 Dihedral : 5.648 26.099 1836 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.31 % Allowed : 9.38 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.20), residues: 1692 helix: 0.16 (0.30), residues: 339 sheet: -2.00 (0.28), residues: 309 loop : -1.37 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 96 HIS 0.008 0.002 HIS A 287 PHE 0.015 0.002 PHE A 376 TYR 0.012 0.002 TYR A 435 ARG 0.004 0.000 ARG I 298 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 443) hydrogen bonds : angle 5.06628 ( 1137) SS BOND : bond 0.00375 ( 36) SS BOND : angle 0.75964 ( 72) covalent geometry : bond 0.00569 (13848) covalent geometry : angle 0.57974 (18789) *********************** 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 166 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 2.030 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 180 ASP cc_start: 0.8794 (m-30) cc_final: 0.8540 (m-30) REVERT: A 412 ARG cc_start: 0.7021 (mtp85) cc_final: 0.6341 (ttp-170) REVERT: A 426 MET cc_start: 0.5603 (mmm) cc_final: 0.4498 (ptt) REVERT: A 480 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7334 (mt-10) REVERT: Z 657 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7276 (mm-30) REVERT: E 267 GLU cc_start: 0.7101 (mp0) cc_final: 0.6824 (mp0) REVERT: E 412 ARG cc_start: 0.7539 (mtp85) cc_final: 0.6431 (ttp-170) REVERT: E 426 MET cc_start: 0.6091 (mmm) cc_final: 0.4793 (ptt) REVERT: E 480 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7073 (mt-10) REVERT: I 84 MET cc_start: 0.7334 (tpt) cc_final: 0.6979 (tpt) REVERT: I 88 ASN cc_start: 0.7772 (t0) cc_final: 0.7441 (t0) REVERT: I 393 ARG cc_start: 0.6054 (mmt180) cc_final: 0.5556 (mtt-85) REVERT: I 412 ARG cc_start: 0.7584 (mtp85) cc_final: 0.6609 (ttp-170) REVERT: I 426 MET cc_start: 0.6006 (mmm) cc_final: 0.4789 (ptt) REVERT: I 477 TRP cc_start: 0.8328 (m-90) cc_final: 0.7791 (m-10) REVERT: J 585 ARG cc_start: 0.7545 (mtt-85) cc_final: 0.7130 (ttp80) REVERT: J 616 ASN cc_start: 0.4449 (t0) cc_final: 0.3900 (p0) outliers start: 20 outliers final: 16 residues processed: 160 average time/residue: 0.6210 time to fit residues: 145.4114 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 : 2.271 ------------------------------------------------------------------------------- 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 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 276 ASN Chi-restraints excluded: chain I residue 327 ARG Chi-restraints excluded: chain I residue 373 THR 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 55 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 540 GLN F 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131011 restraints weight = 474160.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.135297 restraints weight = 284446.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133736 restraints weight = 218350.159| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13884 Z= 0.181 Angle : 0.544 6.538 18861 Z= 0.298 Chirality : 0.044 0.146 2121 Planarity : 0.004 0.057 2397 Dihedral : 5.531 27.930 1836 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.51 % Allowed : 10.70 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1692 helix: 0.24 (0.30), residues: 339 sheet: -1.98 (0.30), residues: 273 loop : -1.44 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 338 HIS 0.008 0.002 HIS I 287 PHE 0.013 0.002 PHE E 93 TYR 0.011 0.001 TYR E 61 ARG 0.002 0.000 ARG F 585 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 443) hydrogen bonds : angle 4.96991 ( 1137) SS BOND : bond 0.00334 ( 36) SS BOND : angle 0.63492 ( 72) covalent geometry : bond 0.00435 (13848) covalent geometry : angle 0.54320 (18789) *********************** 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 161 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 2.146 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: 0.8865 (m-30) cc_final: 0.8600 (m-30) REVERT: A 426 MET cc_start: 0.5830 (mmm) cc_final: 0.4678 (ptt) REVERT: A 480 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7326 (mt-10) REVERT: Z 657 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7049 (mt-10) REVERT: E 267 GLU cc_start: 0.7104 (mp0) cc_final: 0.6774 (mp0) REVERT: E 412 ARG cc_start: 0.7553 (mtp85) cc_final: 0.6466 (ttp-170) REVERT: E 426 MET cc_start: 0.6000 (mmm) cc_final: 0.4699 (ptt) REVERT: E 480 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7060 (mt-10) REVERT: F 571 TRP cc_start: 0.5322 (OUTLIER) cc_final: 0.3049 (m100) REVERT: I 84 MET cc_start: 0.7330 (tpt) cc_final: 0.6984 (tpt) REVERT: I 88 ASN cc_start: 0.7694 (t0) cc_final: 0.7285 (t0) REVERT: I 393 ARG cc_start: 0.6049 (mmt180) cc_final: 0.5744 (mtt-85) REVERT: I 412 ARG cc_start: 0.7536 (mtp85) cc_final: 0.6589 (ttp-170) REVERT: I 426 MET cc_start: 0.5948 (mmm) cc_final: 0.4853 (ptt) REVERT: I 477 TRP cc_start: 0.8335 (m-90) cc_final: 0.7802 (m-10) REVERT: J 585 ARG cc_start: 0.7552 (mtt-85) cc_final: 0.7159 (ttp80) REVERT: J 616 ASN cc_start: 0.4196 (t0) cc_final: 0.3945 (p0) REVERT: J 638 TYR cc_start: 0.6002 (m-80) cc_final: 0.5739 (m-80) outliers start: 23 outliers final: 19 residues processed: 155 average time/residue: 0.6139 time to fit residues: 137.5594 Evaluate side-chains 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 2.047 ------------------------------------------------------------------------------- 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 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 F residue 626 MET Chi-restraints excluded: chain F residue 627 THR 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 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 159 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.158226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131430 restraints weight = 474794.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.134698 restraints weight = 290163.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.134101 restraints weight = 223213.080| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13884 Z= 0.164 Angle : 0.531 6.542 18861 Z= 0.291 Chirality : 0.044 0.145 2121 Planarity : 0.004 0.055 2397 Dihedral : 5.460 27.600 1836 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.31 % Allowed : 11.35 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.20), residues: 1692 helix: 0.23 (0.30), residues: 339 sheet: -2.01 (0.30), residues: 273 loop : -1.47 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 571 HIS 0.006 0.001 HIS I 287 PHE 0.012 0.001 PHE E 93 TYR 0.010 0.001 TYR E 61 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 443) hydrogen bonds : angle 4.93471 ( 1137) SS BOND : bond 0.00281 ( 36) SS BOND : angle 0.82791 ( 72) covalent geometry : bond 0.00395 (13848) covalent geometry : angle 0.52955 (18789) *********************** 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 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 2.281 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: 0.8879 (m-30) cc_final: 0.8606 (m-30) REVERT: A 426 MET cc_start: 0.5863 (mmm) cc_final: 0.4698 (ptt) REVERT: A 480 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7318 (mt-10) REVERT: Z 657 GLU cc_start: 0.7935 (mm-30) cc_final: 0.6108 (tm-30) REVERT: E 267 GLU cc_start: 0.7164 (mp0) cc_final: 0.6835 (mp0) REVERT: E 426 MET cc_start: 0.6134 (mmm) cc_final: 0.4737 (ptt) REVERT: E 480 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7012 (mt-10) REVERT: F 571 TRP cc_start: 0.5352 (OUTLIER) cc_final: 0.3103 (m100) REVERT: I 84 MET cc_start: 0.7345 (tpt) cc_final: 0.7003 (tpt) REVERT: I 88 ASN cc_start: 0.7545 (t0) cc_final: 0.7235 (t0) REVERT: I 393 ARG cc_start: 0.6098 (mmt180) cc_final: 0.5800 (mtt-85) REVERT: I 412 ARG cc_start: 0.7570 (mtp85) cc_final: 0.6617 (ttp-170) REVERT: I 426 MET cc_start: 0.5934 (mmm) cc_final: 0.4746 (ptt) REVERT: I 477 TRP cc_start: 0.8349 (m-90) cc_final: 0.7806 (m-10) REVERT: J 616 ASN cc_start: 0.4423 (t0) cc_final: 0.3942 (p0) REVERT: J 638 TYR cc_start: 0.5991 (m-80) cc_final: 0.5685 (m-80) outliers start: 20 outliers final: 16 residues processed: 147 average time/residue: 0.5946 time to fit residues: 126.9381 Evaluate side-chains 147 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 2.096 ------------------------------------------------------------------------------- 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 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 F residue 627 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 327 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.181497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.158299 restraints weight = 423667.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162074 restraints weight = 242264.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.161320 restraints weight = 190014.271| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13884 Z= 0.095 Angle : 0.478 6.265 18861 Z= 0.259 Chirality : 0.043 0.141 2121 Planarity : 0.004 0.059 2397 Dihedral : 5.081 28.482 1836 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.18 % Allowed : 11.48 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1692 helix: 0.55 (0.30), residues: 339 sheet: -1.48 (0.30), residues: 282 loop : -1.29 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 338 HIS 0.006 0.001 HIS I 287 PHE 0.007 0.001 PHE A 376 TYR 0.008 0.001 TYR A 318 ARG 0.002 0.000 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 443) hydrogen bonds : angle 4.62057 ( 1137) SS BOND : bond 0.00198 ( 36) SS BOND : angle 0.66477 ( 72) covalent geometry : bond 0.00227 (13848) covalent geometry : angle 0.47751 (18789) *********************** 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 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 1.984 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: 0.5796 (mmm) cc_final: 0.4738 (ptt) REVERT: A 480 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7376 (mt-10) REVERT: Z 657 GLU cc_start: 0.7780 (mm-30) cc_final: 0.6039 (tm-30) REVERT: E 267 GLU cc_start: 0.7274 (mp0) cc_final: 0.6883 (mt-10) REVERT: E 426 MET cc_start: 0.5894 (mmm) cc_final: 0.4592 (ptt) REVERT: E 480 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6948 (mt-10) REVERT: F 571 TRP cc_start: 0.5246 (OUTLIER) cc_final: 0.3052 (m100) REVERT: I 84 MET cc_start: 0.7260 (tpt) cc_final: 0.6946 (tpt) REVERT: I 88 ASN cc_start: 0.7603 (t0) cc_final: 0.7269 (t0) REVERT: I 393 ARG cc_start: 0.5979 (mmt180) cc_final: 0.5667 (mtt-85) REVERT: I 412 ARG cc_start: 0.7610 (mtp85) cc_final: 0.6724 (ttp-170) REVERT: I 426 MET cc_start: 0.5892 (mmm) cc_final: 0.4831 (ptt) REVERT: I 477 TRP cc_start: 0.8329 (m-90) cc_final: 0.7846 (m-10) REVERT: J 585 ARG cc_start: 0.7450 (mtt-85) cc_final: 0.7106 (ttp80) REVERT: J 616 ASN cc_start: 0.4305 (t0) cc_final: 0.3915 (p0) outliers start: 18 outliers final: 16 residues processed: 151 average time/residue: 0.5526 time to fit residues: 122.8973 Evaluate side-chains 149 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 Z residue 607 ASN Chi-restraints excluded: chain E residue 37 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 8.9990 chunk 157 optimal weight: 0.0980 chunk 144 optimal weight: 2.9990 chunk 153 optimal weight: 0.0970 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.134277 restraints weight = 470054.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.139531 restraints weight = 283826.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.137018 restraints weight = 211730.102| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13884 Z= 0.100 Angle : 0.476 6.316 18861 Z= 0.259 Chirality : 0.042 0.141 2121 Planarity : 0.004 0.056 2397 Dihedral : 5.004 27.896 1836 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.05 % Allowed : 11.75 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1692 helix: 0.60 (0.30), residues: 339 sheet: -1.32 (0.28), residues: 318 loop : -1.23 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 338 HIS 0.004 0.001 HIS I 287 PHE 0.006 0.001 PHE E 233 TYR 0.008 0.001 TYR E 61 ARG 0.002 0.000 ARG I 502 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 443) hydrogen bonds : angle 4.57313 ( 1137) SS BOND : bond 0.00201 ( 36) SS BOND : angle 0.57251 ( 72) covalent geometry : bond 0.00234 (13848) covalent geometry : angle 0.47607 (18789) *********************** 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 150 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 2.006 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: 0.5824 (mmm) cc_final: 0.4704 (ptt) REVERT: A 480 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7431 (mt-10) REVERT: Z 657 GLU cc_start: 0.7778 (mm-30) cc_final: 0.5960 (tm-30) REVERT: E 267 GLU cc_start: 0.7268 (mp0) cc_final: 0.6803 (mt-10) REVERT: E 426 MET cc_start: 0.6071 (mmm) cc_final: 0.4616 (ptt) REVERT: E 480 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6914 (mt-10) REVERT: F 571 TRP cc_start: 0.5241 (OUTLIER) cc_final: 0.2986 (m100) REVERT: I 84 MET cc_start: 0.7397 (tpt) cc_final: 0.7086 (tpt) REVERT: I 88 ASN cc_start: 0.7630 (t0) cc_final: 0.7299 (t0) REVERT: I 393 ARG cc_start: 0.6019 (mmt180) cc_final: 0.5690 (mtt-85) REVERT: I 412 ARG cc_start: 0.7615 (mtp85) cc_final: 0.6616 (ttp-170) REVERT: I 426 MET cc_start: 0.5887 (mmm) cc_final: 0.4767 (ptt) REVERT: I 477 TRP cc_start: 0.8340 (m-90) cc_final: 0.7903 (m-10) REVERT: J 616 ASN cc_start: 0.4406 (t0) cc_final: 0.3882 (p0) outliers start: 16 outliers final: 13 residues processed: 147 average time/residue: 0.5541 time to fit residues: 119.2670 Evaluate side-chains 145 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.989 ------------------------------------------------------------------------------- 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 E residue 131 CYS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 464 GLU 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 197 ASN 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 162 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 135 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 651 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.159901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132912 restraints weight = 473419.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137475 restraints weight = 272190.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.135498 restraints weight = 211492.352| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13884 Z= 0.131 Angle : 0.491 6.347 18861 Z= 0.267 Chirality : 0.043 0.144 2121 Planarity : 0.004 0.056 2397 Dihedral : 5.034 27.228 1836 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.25 % Allowed : 11.55 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1692 helix: 0.68 (0.31), residues: 339 sheet: -1.55 (0.28), residues: 318 loop : -1.27 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 338 HIS 0.005 0.001 HIS I 287 PHE 0.010 0.001 PHE E 93 TYR 0.009 0.001 TYR E 61 ARG 0.002 0.000 ARG I 502 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 443) hydrogen bonds : angle 4.56766 ( 1137) SS BOND : bond 0.00235 ( 36) SS BOND : angle 0.67473 ( 72) covalent geometry : bond 0.00314 (13848) covalent geometry : angle 0.49023 (18789) ********************** 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 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 2.101 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 412 ARG cc_start: 0.7296 (mtp85) cc_final: 0.6466 (ttp-170) REVERT: A 426 MET cc_start: 0.5876 (mmm) cc_final: 0.4711 (ptt) REVERT: A 480 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7351 (mt-10) REVERT: Z 657 GLU cc_start: 0.7793 (mm-30) cc_final: 0.6028 (tm-30) REVERT: E 267 GLU cc_start: 0.7205 (mp0) cc_final: 0.6824 (mt-10) REVERT: E 426 MET cc_start: 0.5983 (mmm) cc_final: 0.4576 (ptt) REVERT: E 480 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6991 (mt-10) REVERT: F 571 TRP cc_start: 0.5291 (OUTLIER) cc_final: 0.3045 (m100) REVERT: I 84 MET cc_start: 0.7243 (tpt) cc_final: 0.6958 (tpt) REVERT: I 88 ASN cc_start: 0.7769 (t0) cc_final: 0.7453 (t0) REVERT: I 393 ARG cc_start: 0.5934 (mmt180) cc_final: 0.5626 (mtt-85) REVERT: I 426 MET cc_start: 0.6089 (mmm) cc_final: 0.4870 (ptt) REVERT: I 477 TRP cc_start: 0.8359 (m-90) cc_final: 0.7928 (m-10) REVERT: J 616 ASN cc_start: 0.4325 (t0) cc_final: 0.3973 (p0) REVERT: J 638 TYR cc_start: 0.5942 (m-80) cc_final: 0.5664 (m-80) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 0.5842 time to fit residues: 128.1234 Evaluate side-chains 148 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 E residue 37 THR 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 464 GLU 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 197 ASN 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 144 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 651 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134891 restraints weight = 469012.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.138232 restraints weight = 276105.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.137348 restraints weight = 220218.376| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13884 Z= 0.103 Angle : 0.470 6.293 18861 Z= 0.254 Chirality : 0.042 0.141 2121 Planarity : 0.004 0.056 2397 Dihedral : 4.896 27.267 1836 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.98 % Allowed : 11.88 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.20), residues: 1692 helix: 0.77 (0.31), residues: 339 sheet: -1.29 (0.27), residues: 348 loop : -1.20 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 338 HIS 0.004 0.001 HIS I 287 PHE 0.007 0.001 PHE I 93 TYR 0.008 0.001 TYR E 61 ARG 0.002 0.000 ARG F 617 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 443) hydrogen bonds : angle 4.46875 ( 1137) SS BOND : bond 0.00199 ( 36) SS BOND : angle 0.60356 ( 72) covalent geometry : bond 0.00244 (13848) covalent geometry : angle 0.46945 (18789) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6799.74 seconds wall clock time: 118 minutes 28.14 seconds (7108.14 seconds total)