Starting phenix.real_space_refine on Fri Jun 13 18:19:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sw7_40810/06_2025/8sw7_40810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sw7_40810/06_2025/8sw7_40810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sw7_40810/06_2025/8sw7_40810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sw7_40810/06_2025/8sw7_40810.map" model { file = "/net/cci-nas-00/data/ceres_data/8sw7_40810/06_2025/8sw7_40810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sw7_40810/06_2025/8sw7_40810.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9437 2.51 5 N 2600 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15133 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 998 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3424 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 4 Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3365 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 18, 'TRANS': 406} Chain breaks: 5 Chain: "H" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 625 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 9.61, per 1000 atoms: 0.64 Number of scatterers: 15133 At special positions: 0 Unit cell: (128.875, 136.092, 120.627, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2994 8.00 N 2600 7.00 C 9437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.10 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.02 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.06 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 156 " " NAG A 605 " - " ASN A 160 " " NAG A 606 " - " ASN A 197 " " NAG A 607 " - " ASN A 234 " " NAG A 608 " - " ASN A 241 " " NAG A 609 " - " ASN A 276 " " NAG A 610 " - " ASN A 289 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 332 " " NAG A 613 " - " ASN A 392 " " NAG A 614 " - " ASN A 448 " " NAG A 615 " - " ASN A 295 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 241 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 332 " " NAG C 611 " - " ASN C 392 " " NAG C 612 " - " ASN C 448 " " NAG C 613 " - " ASN C 386 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 637 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 241 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 289 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 332 " " NAG F 612 " - " ASN F 386 " " NAG F 613 " - " ASN F 392 " " NAG F 614 " - " ASN F 448 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN F 262 " Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.5 seconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 34 sheets defined 26.6% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.111A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.858A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.123A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.687A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.383A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.627A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.861A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 633 removed outlier: 3.529A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 637 removed outlier: 5.637A pdb=" N ASN D 637 " --> pdb=" O GLU D 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 637' Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.178A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 535 Processing helix chain 'E' and resid 536 through 543 Processing helix chain 'E' and resid 572 through 595 Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.233A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 167 removed outlier: 3.902A pdb=" N ARG F 166 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP F 167 " --> pdb=" O GLU F 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 163 through 167' Processing helix chain 'F' and resid 335 through 351 removed outlier: 4.073A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 476 through 484 removed outlier: 4.239A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.747A pdb=" N UNK H 32 " --> pdb=" O UNK H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.334A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.199A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.706A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.615A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.655A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.712A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.655A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.108A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.721A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 10.342A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.971A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.417A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.143A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.653A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.877A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 170 through 177 removed outlier: 3.651A pdb=" N GLN F 130 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.547A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.922A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 301 through 312 removed outlier: 4.081A pdb=" N ASN F 301 " --> pdb=" O ILE F 323A" (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR F 303 " --> pdb=" O ASP F 322 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP F 322 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS F 305 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR F 320 " --> pdb=" O LYS F 305 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE F 307 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR F 318 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE F 309 " --> pdb=" O TRP F 316 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP F 316 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 7 through 8 Processing sheet with id=AD2, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.569A pdb=" N UNK H 12 " --> pdb=" O UNK H 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.357A pdb=" N UNK H 45 " --> pdb=" O UNK H 40 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N UNK H 40 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N UNK H 34 " --> pdb=" O UNK H 51 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N UNK H 96 " --> pdb=" O UNK H 115 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N UNK H 115 " --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N UNK H 98 " --> pdb=" O UNK H 113 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.357A pdb=" N UNK H 45 " --> pdb=" O UNK H 40 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N UNK H 40 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N UNK H 34 " --> pdb=" O UNK H 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.546A pdb=" N UNK L 11 " --> pdb=" O UNK L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.269A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 3792 1.33 - 1.48: 5118 1.48 - 1.63: 6341 1.63 - 1.78: 52 1.78 - 1.94: 86 Bond restraints: 15389 Sorted by residual: bond pdb=" NE ARG F 504 " pdb=" CZ ARG F 504 " ideal model delta sigma weight residual 1.326 1.406 -0.080 1.10e-02 8.26e+03 5.24e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.42e+01 bond pdb=" CD2 TRP E 571 " pdb=" CE3 TRP E 571 " ideal model delta sigma weight residual 1.398 1.504 -0.106 1.60e-02 3.91e+03 4.36e+01 bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.500 -0.102 1.60e-02 3.91e+03 4.07e+01 bond pdb=" CZ2 TRP E 571 " pdb=" CH2 TRP E 571 " ideal model delta sigma weight residual 1.368 1.489 -0.121 1.90e-02 2.77e+03 4.03e+01 ... (remaining 15384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 17546 2.22 - 4.43: 2810 4.43 - 6.65: 475 6.65 - 8.87: 86 8.87 - 11.08: 9 Bond angle restraints: 20926 Sorted by residual: angle pdb=" N PRO A 437 " pdb=" CA PRO A 437 " pdb=" C PRO A 437 " ideal model delta sigma weight residual 110.58 100.83 9.75 1.07e+00 8.73e-01 8.30e+01 angle pdb=" N ARG F 476 " pdb=" CA ARG F 476 " pdb=" C ARG F 476 " ideal model delta sigma weight residual 114.04 102.96 11.08 1.24e+00 6.50e-01 7.99e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.25 -7.69 1.01e+00 9.80e-01 5.79e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.01e+00 9.80e-01 5.71e+01 angle pdb=" N PRO F 437 " pdb=" CA PRO F 437 " pdb=" C PRO F 437 " ideal model delta sigma weight residual 110.58 102.50 8.08 1.07e+00 8.73e-01 5.71e+01 ... (remaining 20921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 9708 21.13 - 42.27: 204 42.27 - 63.40: 70 63.40 - 84.54: 32 84.54 - 105.67: 15 Dihedral angle restraints: 10029 sinusoidal: 4537 harmonic: 5492 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.83 -81.83 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 140.08 -47.08 1 1.00e+01 1.00e-02 3.06e+01 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 -129.29 43.29 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 10026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1757 0.102 - 0.203: 526 0.203 - 0.304: 170 0.304 - 0.406: 97 0.406 - 0.507: 34 Chirality restraints: 2584 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.84e+01 ... (remaining 2581 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.099 2.00e-02 2.50e+03 1.04e-01 1.35e+02 pdb=" CG ASN D 611 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.161 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.095 2.00e-02 2.50e+03 9.81e-02 1.20e+02 pdb=" CG ASN A 234 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.151 2.00e-02 2.50e+03 pdb=" C1 NAG A 607 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 133 " 0.076 2.00e-02 2.50e+03 7.89e-02 7.77e+01 pdb=" CG ASN C 133 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN C 133 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 133 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " 0.096 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1886 2.73 - 3.27: 14014 3.27 - 3.82: 23448 3.82 - 4.36: 29523 4.36 - 4.90: 47925 Nonbonded interactions: 116796 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.188 3.040 nonbonded pdb=" N UNK H 51 " pdb=" N UNK H 52 " model vdw 2.394 2.560 nonbonded pdb=" NZ LYS C 231 " pdb=" OE1 GLU C 267 " model vdw 2.418 3.120 nonbonded pdb=" N LEU F 125 " pdb=" O LEU F 125 " model vdw 2.419 2.496 nonbonded pdb=" N VAL F 127 " pdb=" O VAL F 127 " model vdw 2.423 2.496 ... (remaining 116791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 457 or resid 463 through 503 or resid 603 through 614)) selection = (chain 'C' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 503 or resid 601 through 612)) selection = (chain 'F' and (resid 32 through 503 or resid 603 through 614)) } ncs_group { reference = (chain 'B' and (resid 522 through 664 or resid 701 through 702)) selection = chain 'D' selection = (chain 'E' and (resid 522 through 664 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.400 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.023 0.145 15480 Z= 1.196 Angle : 1.741 12.204 21166 Z= 1.111 Chirality : 0.133 0.507 2584 Planarity : 0.009 0.052 2613 Dihedral : 11.373 105.669 6352 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 0.14 % Allowed : 0.61 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1622 helix: 0.55 (0.26), residues: 376 sheet: 1.10 (0.25), residues: 398 loop : 0.33 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.009 TRP F 35 HIS 0.010 0.002 HIS C 374 PHE 0.029 0.006 PHE A 353 TYR 0.038 0.007 TYR B 643 ARG 0.009 0.001 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.08112 ( 52) link_NAG-ASN : angle 2.67185 ( 156) link_BETA1-4 : bond 0.07521 ( 6) link_BETA1-4 : angle 4.80451 ( 18) hydrogen bonds : bond 0.15922 ( 555) hydrogen bonds : angle 7.89529 ( 1596) SS BOND : bond 0.01589 ( 33) SS BOND : angle 3.60500 ( 66) covalent geometry : bond 0.02220 (15389) covalent geometry : angle 1.71843 (20926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 599 time to evaluate : 1.608 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 477 ASP cc_start: 0.7926 (m-30) cc_final: 0.7700 (m-30) REVERT: B 627 THR cc_start: 0.8679 (p) cc_final: 0.8456 (t) REVERT: F 474 ASP cc_start: 0.7602 (t70) cc_final: 0.7087 (t70) outliers start: 2 outliers final: 0 residues processed: 601 average time/residue: 0.3006 time to fit residues: 260.4432 Evaluate side-chains 368 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 103 GLN A 195 ASN A 203 GLN A 422 GLN A 425 ASN C 130 GLN C 287 GLN D 607 ASN E 575 GLN E 591 GLN F 203 GLN F 283 ASN F 428 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.165106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139336 restraints weight = 22756.145| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.51 r_work: 0.3553 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15480 Z= 0.182 Angle : 0.823 22.077 21166 Z= 0.400 Chirality : 0.048 0.343 2584 Planarity : 0.004 0.081 2613 Dihedral : 7.978 68.723 3206 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.05 % Allowed : 12.53 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1622 helix: 1.80 (0.28), residues: 360 sheet: 0.65 (0.24), residues: 426 loop : -0.20 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 479 HIS 0.004 0.001 HIS A 249 PHE 0.031 0.002 PHE F 53 TYR 0.038 0.002 TYR E 643 ARG 0.009 0.001 ARG F 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 52) link_NAG-ASN : angle 3.80738 ( 156) link_BETA1-4 : bond 0.00767 ( 6) link_BETA1-4 : angle 3.79252 ( 18) hydrogen bonds : bond 0.06309 ( 555) hydrogen bonds : angle 6.00463 ( 1596) SS BOND : bond 0.00387 ( 33) SS BOND : angle 1.43399 ( 66) covalent geometry : bond 0.00399 (15389) covalent geometry : angle 0.74729 (20926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 427 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8929 (m100) cc_final: 0.7961 (m100) REVERT: A 150 MET cc_start: 0.8245 (mmp) cc_final: 0.7635 (mmt) REVERT: A 258 GLN cc_start: 0.9046 (mt0) cc_final: 0.8735 (mt0) REVERT: A 269 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8349 (mm-30) REVERT: A 452 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8164 (pp) REVERT: B 627 THR cc_start: 0.8821 (p) cc_final: 0.8616 (t) REVERT: C 178 ARG cc_start: 0.8275 (ptm-80) cc_final: 0.8057 (ptm-80) REVERT: C 192 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7779 (tpp-160) REVERT: C 230 ASP cc_start: 0.7735 (t0) cc_final: 0.7532 (t0) REVERT: C 492 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8141 (mt-10) REVERT: D 638 TYR cc_start: 0.8331 (m-80) cc_final: 0.8095 (m-80) REVERT: D 651 ASN cc_start: 0.8746 (t0) cc_final: 0.8540 (t0) REVERT: E 542 ARG cc_start: 0.8782 (ttm170) cc_final: 0.8391 (ttm170) REVERT: E 630 GLN cc_start: 0.8357 (mt0) cc_final: 0.7802 (mt0) REVERT: F 46 LYS cc_start: 0.9005 (mttm) cc_final: 0.8800 (mttp) REVERT: F 153 GLU cc_start: 0.8308 (tp30) cc_final: 0.8049 (tp30) REVERT: F 192 ARG cc_start: 0.7374 (ptt180) cc_final: 0.6830 (ptt180) REVERT: F 368 ASP cc_start: 0.7901 (m-30) cc_final: 0.7642 (p0) outliers start: 45 outliers final: 26 residues processed: 446 average time/residue: 0.2841 time to fit residues: 189.5341 Evaluate side-chains 393 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 366 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 83 optimal weight: 3.9990 chunk 126 optimal weight: 0.0870 chunk 131 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.0770 chunk 175 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 302 ASN C 170 GLN E 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.158395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132870 restraints weight = 23332.368| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.48 r_work: 0.3476 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 15480 Z= 0.243 Angle : 0.790 17.794 21166 Z= 0.386 Chirality : 0.049 0.262 2584 Planarity : 0.004 0.054 2613 Dihedral : 6.969 50.009 3206 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.40 % Allowed : 13.54 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1622 helix: 1.62 (0.28), residues: 363 sheet: 0.27 (0.23), residues: 461 loop : -0.61 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 35 HIS 0.007 0.001 HIS A 72 PHE 0.021 0.002 PHE A 376 TYR 0.018 0.002 TYR A 173 ARG 0.009 0.001 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 52) link_NAG-ASN : angle 3.10087 ( 156) link_BETA1-4 : bond 0.00848 ( 6) link_BETA1-4 : angle 2.93317 ( 18) hydrogen bonds : bond 0.05662 ( 555) hydrogen bonds : angle 5.71027 ( 1596) SS BOND : bond 0.00621 ( 33) SS BOND : angle 1.96174 ( 66) covalent geometry : bond 0.00559 (15389) covalent geometry : angle 0.73529 (20926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 394 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9078 (m100) cc_final: 0.8115 (m100) REVERT: A 269 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8383 (mm-30) REVERT: A 275 GLU cc_start: 0.8731 (tt0) cc_final: 0.8468 (tt0) REVERT: B 624 ASP cc_start: 0.8902 (m-30) cc_final: 0.8622 (t0) REVERT: C 90 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8436 (t) REVERT: C 104 MET cc_start: 0.9372 (ttt) cc_final: 0.9094 (ttt) REVERT: C 178 ARG cc_start: 0.8211 (ptm-80) cc_final: 0.7951 (ptm-80) REVERT: C 191 TYR cc_start: 0.7990 (m-80) cc_final: 0.7678 (m-10) REVERT: C 192 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7422 (tpt170) REVERT: C 394 THR cc_start: 0.7848 (m) cc_final: 0.7543 (t) REVERT: C 492 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8480 (tt0) REVERT: D 530 MET cc_start: 0.6780 (mtt) cc_final: 0.6001 (mtt) REVERT: E 542 ARG cc_start: 0.8809 (ttm170) cc_final: 0.8300 (ttm170) REVERT: E 634 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8186 (tm-30) REVERT: E 645 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8670 (mt) REVERT: E 655 LYS cc_start: 0.8449 (mmtp) cc_final: 0.7816 (mtpp) REVERT: F 153 GLU cc_start: 0.8482 (tp30) cc_final: 0.8186 (tp30) REVERT: F 231 LYS cc_start: 0.8173 (mttt) cc_final: 0.7942 (mmtp) REVERT: F 368 ASP cc_start: 0.8026 (m-30) cc_final: 0.7751 (p0) REVERT: F 377 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7786 (t0) REVERT: F 475 MET cc_start: 0.8992 (mmm) cc_final: 0.8765 (tpp) outliers start: 65 outliers final: 50 residues processed: 427 average time/residue: 0.2584 time to fit residues: 164.5485 Evaluate side-chains 420 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 367 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 649 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 39 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN F 85 HIS F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.160116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134744 restraints weight = 23030.291| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.47 r_work: 0.3495 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15480 Z= 0.161 Angle : 0.689 16.117 21166 Z= 0.332 Chirality : 0.045 0.217 2584 Planarity : 0.003 0.031 2613 Dihedral : 6.039 39.220 3206 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.93 % Allowed : 15.50 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1622 helix: 1.80 (0.28), residues: 365 sheet: 0.23 (0.24), residues: 440 loop : -0.71 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 35 HIS 0.004 0.001 HIS C 249 PHE 0.017 0.002 PHE F 53 TYR 0.015 0.002 TYR F 484 ARG 0.005 0.000 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 52) link_NAG-ASN : angle 2.85511 ( 156) link_BETA1-4 : bond 0.00590 ( 6) link_BETA1-4 : angle 2.60529 ( 18) hydrogen bonds : bond 0.04907 ( 555) hydrogen bonds : angle 5.47160 ( 1596) SS BOND : bond 0.00405 ( 33) SS BOND : angle 1.69302 ( 66) covalent geometry : bond 0.00366 (15389) covalent geometry : angle 0.63550 (20926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 384 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9067 (m100) cc_final: 0.8100 (m100) REVERT: A 275 GLU cc_start: 0.8729 (tt0) cc_final: 0.8362 (tt0) REVERT: A 428 GLN cc_start: 0.8675 (mt0) cc_final: 0.8306 (mm110) REVERT: B 540 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.6233 (mp10) REVERT: C 104 MET cc_start: 0.9338 (ttt) cc_final: 0.9071 (ttt) REVERT: C 150 MET cc_start: 0.7905 (mtp) cc_final: 0.7444 (mtm) REVERT: C 178 ARG cc_start: 0.8278 (ptm-80) cc_final: 0.8066 (ptm-80) REVERT: C 191 TYR cc_start: 0.7991 (m-80) cc_final: 0.7513 (m-10) REVERT: C 192 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7726 (tpt170) REVERT: C 394 THR cc_start: 0.7939 (m) cc_final: 0.7529 (t) REVERT: D 530 MET cc_start: 0.6799 (mtt) cc_final: 0.6047 (mtt) REVERT: E 542 ARG cc_start: 0.8765 (ttm170) cc_final: 0.8157 (ttm170) REVERT: E 634 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8175 (tm-30) REVERT: F 107 ASP cc_start: 0.8672 (m-30) cc_final: 0.8224 (m-30) REVERT: F 112 TRP cc_start: 0.8274 (t-100) cc_final: 0.8005 (t-100) REVERT: F 153 GLU cc_start: 0.8417 (tp30) cc_final: 0.8171 (tp30) REVERT: F 274 SER cc_start: 0.8818 (t) cc_final: 0.8547 (p) REVERT: F 368 ASP cc_start: 0.8085 (m-30) cc_final: 0.7774 (p0) REVERT: F 377 ASN cc_start: 0.8174 (p0) cc_final: 0.7947 (t0) REVERT: F 456 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7555 (mtp85) REVERT: F 475 MET cc_start: 0.9019 (mmm) cc_final: 0.8559 (tpp) outliers start: 58 outliers final: 46 residues processed: 415 average time/residue: 0.2797 time to fit residues: 174.1981 Evaluate side-chains 390 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 343 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 102 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN F 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.158818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133769 restraints weight = 23550.866| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.41 r_work: 0.3517 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15480 Z= 0.225 Angle : 0.722 15.465 21166 Z= 0.350 Chirality : 0.047 0.218 2584 Planarity : 0.004 0.032 2613 Dihedral : 6.055 42.157 3206 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.81 % Allowed : 15.98 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1622 helix: 1.67 (0.28), residues: 365 sheet: 0.04 (0.23), residues: 444 loop : -0.87 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 35 HIS 0.005 0.001 HIS A 330 PHE 0.020 0.002 PHE A 376 TYR 0.016 0.002 TYR F 191 ARG 0.005 0.001 ARG C 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 52) link_NAG-ASN : angle 2.81330 ( 156) link_BETA1-4 : bond 0.00700 ( 6) link_BETA1-4 : angle 2.36205 ( 18) hydrogen bonds : bond 0.05036 ( 555) hydrogen bonds : angle 5.51567 ( 1596) SS BOND : bond 0.00497 ( 33) SS BOND : angle 1.37925 ( 66) covalent geometry : bond 0.00519 (15389) covalent geometry : angle 0.67682 (20926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 350 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9102 (m100) cc_final: 0.8215 (m100) REVERT: A 102 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8187 (mm-30) REVERT: A 428 GLN cc_start: 0.8658 (mt0) cc_final: 0.8384 (mm110) REVERT: B 540 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6524 (mp10) REVERT: C 104 MET cc_start: 0.9402 (ttt) cc_final: 0.9140 (ttt) REVERT: C 178 ARG cc_start: 0.8336 (ptm-80) cc_final: 0.8113 (ptm-80) REVERT: C 191 TYR cc_start: 0.8170 (m-80) cc_final: 0.7788 (m-10) REVERT: C 192 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7518 (tpt170) REVERT: C 196 CYS cc_start: 0.7370 (t) cc_final: 0.7098 (t) REVERT: C 394 THR cc_start: 0.7734 (m) cc_final: 0.7371 (t) REVERT: D 530 MET cc_start: 0.6936 (mtt) cc_final: 0.6233 (mtt) REVERT: D 663 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7243 (mp) REVERT: E 542 ARG cc_start: 0.8786 (ttm170) cc_final: 0.8499 (ttm170) REVERT: E 634 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8203 (tm-30) REVERT: F 35 TRP cc_start: 0.8188 (m100) cc_final: 0.7970 (m100) REVERT: F 107 ASP cc_start: 0.8697 (m-30) cc_final: 0.8290 (m-30) REVERT: F 112 TRP cc_start: 0.8502 (t-100) cc_final: 0.8104 (t-100) REVERT: F 274 SER cc_start: 0.8980 (t) cc_final: 0.8737 (p) REVERT: F 475 MET cc_start: 0.9010 (mmm) cc_final: 0.8716 (tpp) outliers start: 71 outliers final: 58 residues processed: 387 average time/residue: 0.2617 time to fit residues: 151.8234 Evaluate side-chains 392 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 332 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 93 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 258 GLN E 543 ASN E 653 GLN F 283 ASN F 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133266 restraints weight = 23690.606| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.47 r_work: 0.3504 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15480 Z= 0.217 Angle : 0.704 15.285 21166 Z= 0.343 Chirality : 0.046 0.214 2584 Planarity : 0.004 0.049 2613 Dihedral : 6.019 42.786 3206 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.74 % Allowed : 16.66 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1622 helix: 1.62 (0.28), residues: 365 sheet: -0.16 (0.24), residues: 427 loop : -1.03 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 45 HIS 0.004 0.001 HIS A 330 PHE 0.018 0.002 PHE A 376 TYR 0.020 0.002 TYR F 484 ARG 0.006 0.001 ARG A 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 52) link_NAG-ASN : angle 2.68200 ( 156) link_BETA1-4 : bond 0.00638 ( 6) link_BETA1-4 : angle 2.02349 ( 18) hydrogen bonds : bond 0.04915 ( 555) hydrogen bonds : angle 5.47268 ( 1596) SS BOND : bond 0.00685 ( 33) SS BOND : angle 1.46192 ( 66) covalent geometry : bond 0.00501 (15389) covalent geometry : angle 0.66185 (20926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 352 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9154 (m100) cc_final: 0.8247 (m100) REVERT: A 51 THR cc_start: 0.9271 (m) cc_final: 0.8910 (p) REVERT: A 102 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8270 (mm-30) REVERT: A 428 GLN cc_start: 0.8604 (mt0) cc_final: 0.8369 (mm110) REVERT: A 453 ILE cc_start: 0.8161 (mt) cc_final: 0.7772 (tt) REVERT: B 540 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.6600 (mp10) REVERT: C 104 MET cc_start: 0.9382 (ttt) cc_final: 0.9129 (ttt) REVERT: C 178 ARG cc_start: 0.8335 (ptm-80) cc_final: 0.8108 (ptm-80) REVERT: C 191 TYR cc_start: 0.8182 (m-80) cc_final: 0.7930 (m-10) REVERT: C 192 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7158 (tpt170) REVERT: C 394 THR cc_start: 0.7742 (m) cc_final: 0.7415 (t) REVERT: D 530 MET cc_start: 0.7137 (mtt) cc_final: 0.6502 (mtt) REVERT: D 599 SER cc_start: 0.9434 (t) cc_final: 0.9052 (p) REVERT: D 663 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7128 (mp) REVERT: E 530 MET cc_start: 0.8956 (mtm) cc_final: 0.8571 (mtm) REVERT: E 543 ASN cc_start: 0.8696 (m-40) cc_final: 0.8340 (m-40) REVERT: E 634 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8215 (tm-30) REVERT: E 643 TYR cc_start: 0.9170 (m-10) cc_final: 0.8948 (m-80) REVERT: F 35 TRP cc_start: 0.8283 (m100) cc_final: 0.8037 (m100) REVERT: F 87 GLU cc_start: 0.7816 (mp0) cc_final: 0.7391 (mp0) REVERT: F 107 ASP cc_start: 0.8697 (m-30) cc_final: 0.8314 (m-30) REVERT: F 112 TRP cc_start: 0.8515 (t-100) cc_final: 0.8053 (t-100) REVERT: F 231 LYS cc_start: 0.8199 (mttt) cc_final: 0.7725 (mttm) REVERT: F 274 SER cc_start: 0.8680 (t) cc_final: 0.8287 (p) REVERT: F 484 TYR cc_start: 0.8935 (p90) cc_final: 0.8644 (p90) outliers start: 70 outliers final: 60 residues processed: 391 average time/residue: 0.2812 time to fit residues: 164.8489 Evaluate side-chains 399 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 337 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 104 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 630 GLN F 203 GLN F 283 ASN F 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136622 restraints weight = 23863.632| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.55 r_work: 0.3543 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15480 Z= 0.135 Angle : 0.644 14.777 21166 Z= 0.313 Chirality : 0.044 0.209 2584 Planarity : 0.003 0.029 2613 Dihedral : 5.546 39.098 3206 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.13 % Allowed : 18.14 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1622 helix: 1.92 (0.29), residues: 365 sheet: -0.10 (0.24), residues: 444 loop : -1.06 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 96 HIS 0.007 0.001 HIS C 352 PHE 0.014 0.001 PHE A 53 TYR 0.017 0.002 TYR C 486 ARG 0.004 0.000 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 52) link_NAG-ASN : angle 2.54626 ( 156) link_BETA1-4 : bond 0.00616 ( 6) link_BETA1-4 : angle 1.78922 ( 18) hydrogen bonds : bond 0.04355 ( 555) hydrogen bonds : angle 5.25582 ( 1596) SS BOND : bond 0.00486 ( 33) SS BOND : angle 1.67735 ( 66) covalent geometry : bond 0.00302 (15389) covalent geometry : angle 0.59963 (20926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 370 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9128 (m100) cc_final: 0.8261 (m100) REVERT: A 51 THR cc_start: 0.9251 (m) cc_final: 0.8894 (p) REVERT: A 102 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8248 (mm-30) REVERT: A 269 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 440 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: B 540 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6492 (mp10) REVERT: C 104 MET cc_start: 0.9360 (ttt) cc_final: 0.9107 (ttt) REVERT: C 178 ARG cc_start: 0.8270 (ptm-80) cc_final: 0.8022 (ptm-80) REVERT: C 191 TYR cc_start: 0.8160 (m-80) cc_final: 0.7715 (m-10) REVERT: C 192 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7383 (tpt170) REVERT: C 394 THR cc_start: 0.7743 (m) cc_final: 0.7432 (t) REVERT: D 530 MET cc_start: 0.7242 (mtt) cc_final: 0.6626 (mtt) REVERT: D 663 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7048 (mp) REVERT: E 634 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8204 (tm-30) REVERT: F 35 TRP cc_start: 0.8218 (m100) cc_final: 0.7970 (m100) REVERT: F 87 GLU cc_start: 0.7567 (mp0) cc_final: 0.7219 (mp0) REVERT: F 107 ASP cc_start: 0.8688 (m-30) cc_final: 0.8287 (m-30) REVERT: F 112 TRP cc_start: 0.8441 (t-100) cc_final: 0.8035 (t-100) REVERT: F 192 ARG cc_start: 0.7419 (ptt180) cc_final: 0.6966 (ptt180) REVERT: F 231 LYS cc_start: 0.8175 (mttt) cc_final: 0.7721 (mttm) REVERT: F 484 TYR cc_start: 0.8830 (p90) cc_final: 0.8598 (p90) outliers start: 61 outliers final: 47 residues processed: 400 average time/residue: 0.2897 time to fit residues: 174.1282 Evaluate side-chains 398 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 348 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 129 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 425 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136288 restraints weight = 23729.785| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.52 r_work: 0.3539 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15480 Z= 0.150 Angle : 0.646 14.531 21166 Z= 0.317 Chirality : 0.044 0.182 2584 Planarity : 0.003 0.030 2613 Dihedral : 5.498 39.768 3206 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.20 % Allowed : 19.16 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1622 helix: 1.93 (0.29), residues: 366 sheet: -0.13 (0.24), residues: 447 loop : -1.08 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 614 HIS 0.006 0.001 HIS C 352 PHE 0.015 0.002 PHE A 376 TYR 0.015 0.001 TYR F 484 ARG 0.010 0.001 ARG A 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 52) link_NAG-ASN : angle 2.41912 ( 156) link_BETA1-4 : bond 0.00633 ( 6) link_BETA1-4 : angle 1.74124 ( 18) hydrogen bonds : bond 0.04349 ( 555) hydrogen bonds : angle 5.19891 ( 1596) SS BOND : bond 0.00528 ( 33) SS BOND : angle 1.36375 ( 66) covalent geometry : bond 0.00343 (15389) covalent geometry : angle 0.60859 (20926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 352 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9147 (m100) cc_final: 0.8281 (m100) REVERT: A 51 THR cc_start: 0.9281 (m) cc_final: 0.8940 (p) REVERT: A 440 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: C 104 MET cc_start: 0.9349 (ttt) cc_final: 0.9091 (ttt) REVERT: C 178 ARG cc_start: 0.8271 (ptm-80) cc_final: 0.8018 (ptm-80) REVERT: C 192 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7473 (tpt170) REVERT: C 394 THR cc_start: 0.7666 (m) cc_final: 0.7410 (t) REVERT: D 530 MET cc_start: 0.7048 (mtt) cc_final: 0.6490 (mtt) REVERT: D 663 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7052 (mp) REVERT: E 626 MET cc_start: 0.7764 (ttt) cc_final: 0.7321 (ttt) REVERT: E 634 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8231 (tm-30) REVERT: F 35 TRP cc_start: 0.8258 (m100) cc_final: 0.7991 (m100) REVERT: F 87 GLU cc_start: 0.7594 (mp0) cc_final: 0.7228 (mp0) REVERT: F 107 ASP cc_start: 0.8697 (m-30) cc_final: 0.8272 (m-30) REVERT: F 192 ARG cc_start: 0.7425 (ptt180) cc_final: 0.6976 (ptt180) REVERT: F 231 LYS cc_start: 0.8058 (mttt) cc_final: 0.7641 (mttm) REVERT: F 256 SER cc_start: 0.8863 (t) cc_final: 0.8546 (p) REVERT: F 484 TYR cc_start: 0.8910 (p90) cc_final: 0.8657 (p90) outliers start: 62 outliers final: 53 residues processed: 388 average time/residue: 0.2456 time to fit residues: 143.5786 Evaluate side-chains 397 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 148 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN E 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133044 restraints weight = 23224.677| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.41 r_work: 0.3488 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15480 Z= 0.192 Angle : 0.674 14.213 21166 Z= 0.331 Chirality : 0.045 0.190 2584 Planarity : 0.004 0.036 2613 Dihedral : 5.757 41.595 3206 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.60 % Allowed : 19.16 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1622 helix: 1.80 (0.28), residues: 371 sheet: -0.15 (0.24), residues: 446 loop : -1.17 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 614 HIS 0.007 0.001 HIS A 72 PHE 0.017 0.002 PHE A 376 TYR 0.017 0.002 TYR F 191 ARG 0.009 0.001 ARG A 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 52) link_NAG-ASN : angle 2.44496 ( 156) link_BETA1-4 : bond 0.00648 ( 6) link_BETA1-4 : angle 1.77716 ( 18) hydrogen bonds : bond 0.04597 ( 555) hydrogen bonds : angle 5.30025 ( 1596) SS BOND : bond 0.00527 ( 33) SS BOND : angle 1.43686 ( 66) covalent geometry : bond 0.00446 (15389) covalent geometry : angle 0.63725 (20926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 352 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9178 (m100) cc_final: 0.8336 (m100) REVERT: A 51 THR cc_start: 0.9276 (m) cc_final: 0.8938 (p) REVERT: A 102 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8284 (mm-30) REVERT: A 440 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: C 104 MET cc_start: 0.9360 (ttt) cc_final: 0.9116 (ttt) REVERT: C 178 ARG cc_start: 0.8258 (ptm-80) cc_final: 0.8005 (ptm-80) REVERT: C 394 THR cc_start: 0.7722 (m) cc_final: 0.7451 (t) REVERT: C 426 MET cc_start: 0.8468 (mmm) cc_final: 0.8199 (mmm) REVERT: D 530 MET cc_start: 0.7035 (mtt) cc_final: 0.6496 (mtt) REVERT: D 599 SER cc_start: 0.9382 (t) cc_final: 0.8964 (p) REVERT: D 663 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7164 (mp) REVERT: E 542 ARG cc_start: 0.8725 (ttm170) cc_final: 0.8410 (ttm170) REVERT: E 621 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6678 (tp30) REVERT: F 35 TRP cc_start: 0.8258 (m100) cc_final: 0.8009 (m100) REVERT: F 87 GLU cc_start: 0.7835 (mp0) cc_final: 0.7459 (mp0) REVERT: F 107 ASP cc_start: 0.8700 (m-30) cc_final: 0.8302 (m-30) REVERT: F 231 LYS cc_start: 0.8069 (mttt) cc_final: 0.7680 (mttm) REVERT: F 256 SER cc_start: 0.8970 (t) cc_final: 0.8649 (p) REVERT: F 484 TYR cc_start: 0.8966 (p90) cc_final: 0.8707 (p90) outliers start: 68 outliers final: 60 residues processed: 391 average time/residue: 0.2451 time to fit residues: 144.0390 Evaluate side-chains 411 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 349 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 630 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 12 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 85 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN E 630 GLN F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.160362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134282 restraints weight = 23831.124| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.59 r_work: 0.3508 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15480 Z= 0.132 Angle : 0.644 14.418 21166 Z= 0.314 Chirality : 0.044 0.195 2584 Planarity : 0.003 0.044 2613 Dihedral : 5.499 39.478 3206 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.79 % Allowed : 20.51 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1622 helix: 2.01 (0.29), residues: 365 sheet: -0.07 (0.24), residues: 443 loop : -1.14 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 623 HIS 0.005 0.001 HIS C 352 PHE 0.012 0.001 PHE A 376 TYR 0.017 0.001 TYR C 191 ARG 0.009 0.000 ARG A 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 52) link_NAG-ASN : angle 2.33548 ( 156) link_BETA1-4 : bond 0.00604 ( 6) link_BETA1-4 : angle 1.68364 ( 18) hydrogen bonds : bond 0.04256 ( 555) hydrogen bonds : angle 5.18315 ( 1596) SS BOND : bond 0.00483 ( 33) SS BOND : angle 1.42138 ( 66) covalent geometry : bond 0.00296 (15389) covalent geometry : angle 0.60858 (20926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 343 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9154 (m100) cc_final: 0.8257 (m100) REVERT: A 51 THR cc_start: 0.9260 (m) cc_final: 0.8985 (p) REVERT: A 102 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8280 (mm-30) REVERT: B 540 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: C 104 MET cc_start: 0.9306 (ttt) cc_final: 0.9057 (ttt) REVERT: C 178 ARG cc_start: 0.8238 (ptm-80) cc_final: 0.7983 (ptm-80) REVERT: C 348 GLN cc_start: 0.7905 (tp40) cc_final: 0.7376 (tp40) REVERT: C 394 THR cc_start: 0.7728 (m) cc_final: 0.7459 (t) REVERT: C 426 MET cc_start: 0.8488 (mmm) cc_final: 0.8217 (mmm) REVERT: C 499 THR cc_start: 0.8208 (t) cc_final: 0.7800 (m) REVERT: C 502 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7642 (ttmm) REVERT: D 588 ARG cc_start: 0.8602 (ttt180) cc_final: 0.8194 (ttm-80) REVERT: D 663 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7101 (mp) REVERT: E 621 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6578 (tp30) REVERT: F 35 TRP cc_start: 0.8257 (m100) cc_final: 0.7957 (m100) REVERT: F 87 GLU cc_start: 0.7680 (mp0) cc_final: 0.7325 (mp0) REVERT: F 107 ASP cc_start: 0.8710 (m-30) cc_final: 0.8285 (m-30) REVERT: F 231 LYS cc_start: 0.8017 (mttt) cc_final: 0.7602 (mttm) REVERT: F 248 THR cc_start: 0.8726 (m) cc_final: 0.8465 (p) REVERT: F 256 SER cc_start: 0.8907 (t) cc_final: 0.8592 (p) REVERT: F 484 TYR cc_start: 0.8901 (p90) cc_final: 0.8670 (p90) outliers start: 56 outliers final: 51 residues processed: 375 average time/residue: 0.2848 time to fit residues: 159.9599 Evaluate side-chains 391 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 337 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 630 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.159561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133538 restraints weight = 23905.849| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.56 r_work: 0.3499 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15480 Z= 0.157 Angle : 0.647 14.196 21166 Z= 0.316 Chirality : 0.044 0.184 2584 Planarity : 0.003 0.045 2613 Dihedral : 5.532 40.182 3206 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.99 % Allowed : 20.24 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1622 helix: 1.92 (0.28), residues: 371 sheet: -0.07 (0.24), residues: 450 loop : -1.21 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 631 HIS 0.005 0.001 HIS C 352 PHE 0.029 0.002 PHE A 361 TYR 0.019 0.002 TYR C 191 ARG 0.009 0.000 ARG A 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 52) link_NAG-ASN : angle 2.31620 ( 156) link_BETA1-4 : bond 0.00629 ( 6) link_BETA1-4 : angle 1.67872 ( 18) hydrogen bonds : bond 0.04322 ( 555) hydrogen bonds : angle 5.15766 ( 1596) SS BOND : bond 0.00486 ( 33) SS BOND : angle 1.29106 ( 66) covalent geometry : bond 0.00361 (15389) covalent geometry : angle 0.61259 (20926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7693.97 seconds wall clock time: 137 minutes 46.48 seconds (8266.48 seconds total)