Starting phenix.real_space_refine on Thu Sep 18 07:47:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhk_49414/09_2025/9nhk_49414.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhk_49414/09_2025/9nhk_49414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nhk_49414/09_2025/9nhk_49414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhk_49414/09_2025/9nhk_49414.map" model { file = "/net/cci-nas-00/data/ceres_data/9nhk_49414/09_2025/9nhk_49414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhk_49414/09_2025/9nhk_49414.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.025 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 101 5.16 5 C 9318 2.51 5 N 2512 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14953 Number of models: 1 Model: "" Number of chains: 19 Chain: "H" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 610 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'UNK:plan-1': 114} Unresolved non-hydrogen planarities: 114 Chain: "L" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 545 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'UNK:plan-1': 104} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3293 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 20, 'TRANS': 400} Chain breaks: 4 Chain: "D" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 893 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain breaks: 1 Chain: "A" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3368 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 20, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 915 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "E" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3390 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 3 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 982 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 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: 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: "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: "K" 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: "M" 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: "C" 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: "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: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.42, per 1000 atoms: 0.23 Number of scatterers: 14953 At special positions: 0 Unit cell: (125.35, 123.05, 150.65, 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 101 16.00 O 3022 8.00 N 2512 7.00 C 9318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 500 " - pdb=" SG CYS B 663 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 663 " - pdb=" SG CYS E 500 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS F 663 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " NAG K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 230 " " NAG A 606 " - " ASN A 289 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 385 " " NAG A 610 " - " ASN A 442 " " NAG A 611 " - " ASN A 448 " " NAG A 612 " - " ASN A 357 " " NAG A 613 " - " ASN A 391 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 88 " " NAG A 616 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 616 " " NAG B 704 " - " ASN B 656 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 230 " " NAG C 606 " - " ASN C 241 " " NAG C 607 " - " ASN C 289 " " NAG C 609 " - " ASN C 332 " " NAG C 610 " - " ASN C 385 " " NAG C 611 " - " ASN C 442 " " NAG C 612 " - " ASN C 448 " " NAG C 613 " - " ASN C 133 " " NAG C 614 " - " ASN C 88 " " NAG C 615 " - " ASN C 339 " " NAG D 701 " - " ASN D 656 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 130 " " NAG E 602 " - " ASN E 156 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 230 " " NAG E 606 " - " ASN E 289 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 332 " " NAG E 609 " - " ASN E 442 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 88 " " NAG E 612 " - " ASN E 133 " " NAG E 613 " - " ASN E 391 " " NAG E 614 " - " ASN E 385 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG F 703 " - " ASN F 656 " " NAG F 704 " - " ASN F 616 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN A 241 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN E 241 " " NAG M 1 " - " ASN E 262 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 577.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3502 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 30 sheets defined 24.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.546A 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 353 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 481 through 483 No H-bonds generated for 'chain 'C' and resid 481 through 483' Processing helix chain 'D' and resid 533 through 537 removed outlier: 3.777A pdb=" N THR D 536 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 537 " --> pdb=" O SER D 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 537' Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 612 through 616 removed outlier: 3.597A pdb=" N SER D 615 " --> pdb=" O SER D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 636 through 642 removed outlier: 3.908A pdb=" N THR D 639 " --> pdb=" O SER D 636 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 658 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.821A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 475 through 483 removed outlier: 4.485A pdb=" N GLU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.243A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.722A pdb=" N GLU E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.931A pdb=" N SER E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 660 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'H' and resid 55 through 59 removed outlier: 4.851A pdb=" N UNK H 57 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N UNK H 50 " --> pdb=" O UNK H 57 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N UNK H 59 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N UNK H 48 " --> pdb=" O UNK H 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N CYS H 93 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP H 108 " --> pdb=" O CYS H 93 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N UNK H 95 " --> pdb=" O UNK H 106 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N UNK H 106 " --> pdb=" O UNK H 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA7, first strand: chain 'L' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 498 removed outlier: 5.139A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.605A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 308 removed outlier: 5.462A pdb=" N THR C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N THR C 320 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 324 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 469 Processing sheet with id=AB6, first strand: chain 'A' and resid 493 through 498 removed outlier: 5.285A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AC2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.814A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 4.042A pdb=" N GLN A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 324 current: chain 'A' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 380 through 384 current: chain 'A' and resid 464 through 469 Processing sheet with id=AC5, first strand: chain 'E' and resid 493 through 498 removed outlier: 5.445A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 120 through 121 removed outlier: 3.853A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 283 through 298 removed outlier: 7.428A pdb=" N LYS E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 330 through 334 current: chain 'E' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 380 through 384 current: chain 'E' and resid 466 through 468 Processing sheet with id=AD3, first strand: chain 'E' and resid 300 through 308 removed outlier: 6.663A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1176 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: 2.20 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2957 1.32 - 1.46: 5053 1.46 - 1.60: 7049 1.60 - 1.74: 31 1.74 - 1.88: 128 Bond restraints: 15218 Sorted by residual: bond pdb=" CB HIS C 72 " pdb=" CG HIS C 72 " ideal model delta sigma weight residual 1.497 1.599 -0.102 1.40e-02 5.10e+03 5.30e+01 bond pdb=" CB HIS E 373 " pdb=" CG HIS E 373 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.04e+01 bond pdb=" CZ2 TRP A 394 " pdb=" CH2 TRP A 394 " ideal model delta sigma weight residual 1.368 1.477 -0.109 1.90e-02 2.77e+03 3.27e+01 bond pdb=" CD2 TRP C 394 " pdb=" CE3 TRP C 394 " ideal model delta sigma weight residual 1.398 1.489 -0.091 1.60e-02 3.91e+03 3.23e+01 bond pdb=" CZ2 TRP E 394 " pdb=" CH2 TRP E 394 " ideal model delta sigma weight residual 1.368 1.475 -0.107 1.90e-02 2.77e+03 3.15e+01 ... (remaining 15213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 18270 2.55 - 5.11: 2141 5.11 - 7.66: 264 7.66 - 10.22: 34 10.22 - 12.77: 7 Bond angle restraints: 20716 Sorted by residual: angle pdb=" N LYS C 207 " pdb=" CA LYS C 207 " pdb=" C LYS C 207 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.49e+01 angle pdb=" N GLY B 524 " pdb=" CA GLY B 524 " pdb=" C GLY B 524 " ideal model delta sigma weight residual 112.14 101.07 11.07 1.29e+00 6.01e-01 7.37e+01 angle pdb=" N ILE F 622 " pdb=" CA ILE F 622 " pdb=" C ILE F 622 " ideal model delta sigma weight residual 111.56 104.24 7.32 8.60e-01 1.35e+00 7.25e+01 angle pdb=" N ILE D 642 " pdb=" CA ILE D 642 " pdb=" C ILE D 642 " ideal model delta sigma weight residual 111.67 103.85 7.82 9.50e-01 1.11e+00 6.77e+01 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.02e+00 9.61e-01 6.73e+01 ... (remaining 20711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 9736 21.11 - 42.22: 186 42.22 - 63.33: 59 63.33 - 84.44: 29 84.44 - 105.54: 18 Dihedral angle restraints: 10028 sinusoidal: 4647 harmonic: 5381 Sorted by residual: dihedral pdb=" CB CYS C 377 " pdb=" SG CYS C 377 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual 93.00 153.14 -60.14 1 1.00e+01 1.00e-02 4.82e+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 -129.13 43.13 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -123.99 37.99 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 10025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1821 0.109 - 0.217: 471 0.217 - 0.326: 188 0.326 - 0.435: 89 0.435 - 0.543: 30 Chirality restraints: 2599 Sorted by residual: chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.21e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.03e+02 ... (remaining 2596 not shown) Planarity restraints: 2619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 609 " -0.223 2.00e-02 2.50e+03 1.86e-01 4.34e+02 pdb=" C7 NAG E 609 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG E 609 " -0.156 2.00e-02 2.50e+03 pdb=" N2 NAG E 609 " 0.310 2.00e-02 2.50e+03 pdb=" O7 NAG E 609 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 608 " -0.165 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" C7 NAG C 608 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG C 608 " -0.122 2.00e-02 2.50e+03 pdb=" N2 NAG C 608 " 0.217 2.00e-02 2.50e+03 pdb=" O7 NAG C 608 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 133 " -0.093 2.00e-02 2.50e+03 9.77e-02 1.19e+02 pdb=" CG ASN A 133 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 133 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 133 " 0.151 2.00e-02 2.50e+03 pdb=" C1 NAG A 616 " -0.118 2.00e-02 2.50e+03 ... (remaining 2616 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5177 2.87 - 3.37: 13787 3.37 - 3.88: 24588 3.88 - 4.39: 28242 4.39 - 4.90: 44570 Nonbonded interactions: 116364 Sorted by model distance: nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.358 2.496 nonbonded pdb=" N GLN C 258 " pdb=" O GLN C 258 " model vdw 2.367 2.496 nonbonded pdb=" NZ LYS E 46 " pdb=" OD2 ASP F 632 " model vdw 2.381 3.120 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.381 2.496 nonbonded pdb=" N LYS C 207 " pdb=" N VAL C 208 " model vdw 2.384 2.560 ... (remaining 116359 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 33 through 66 or resid 73 through 77 or resid 82 through 5 \ 04 or resid 602 through 614)) selection = (chain 'C' and resid 33 through 613) selection = (chain 'E' and (resid 33 through 66 or resid 73 through 77 or resid 82 through 5 \ 04 or resid 602 through 614)) } ncs_group { reference = (chain 'B' and (resid 524 through 538 or resid 568 through 663 or resid 702 thro \ ugh 703)) selection = (chain 'D' and (resid 524 through 663 or resid 701 through 702)) selection = (chain 'F' and (resid 524 through 538 or resid 568 through 663 or resid 702 thro \ ugh 703)) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) } ncs_group { reference = (chain 'H' and (resid 1 through 21 or resid 24 through 92 or resid 101 through 1 \ 07 or resid 109 through 116)) selection = (chain 'L' and (resid 2 through 98 or resid 100 through 107)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.580 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.240 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.022 0.134 15320 Z= 1.149 Angle : 1.740 12.772 20988 Z= 1.101 Chirality : 0.138 0.543 2599 Planarity : 0.010 0.186 2560 Dihedral : 11.298 105.545 6424 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1595 helix: 0.46 (0.25), residues: 355 sheet: 0.80 (0.23), residues: 412 loop : 0.43 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 468 TYR 0.039 0.007 TYR C 485 PHE 0.037 0.007 PHE C 382 TRP 0.068 0.011 TRP C 35 HIS 0.007 0.002 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.02113 (15218) covalent geometry : angle 1.71823 (20716) SS BOND : bond 0.00740 ( 34) SS BOND : angle 2.43841 ( 68) hydrogen bonds : bond 0.15407 ( 444) hydrogen bonds : angle 7.49777 ( 1176) link_BETA1-4 : bond 0.07106 ( 9) link_BETA1-4 : angle 4.87250 ( 27) link_NAG-ASN : bond 0.08057 ( 59) link_NAG-ASN : angle 2.75476 ( 177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.593 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: C 42 VAL cc_start: 0.9456 (t) cc_final: 0.9165 (p) REVERT: C 180 ASP cc_start: 0.8892 (m-30) cc_final: 0.8541 (m-30) REVERT: C 256 SER cc_start: 0.9484 (p) cc_final: 0.9140 (t) REVERT: C 439 ILE cc_start: 0.8738 (mt) cc_final: 0.8441 (mm) REVERT: D 586 TYR cc_start: 0.9542 (t80) cc_final: 0.9342 (t80) REVERT: A 210 PHE cc_start: 0.8758 (m-80) cc_final: 0.8255 (m-10) REVERT: B 584 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8664 (tm-30) REVERT: E 217 TYR cc_start: 0.9154 (m-80) cc_final: 0.8692 (m-80) REVERT: E 484 LYS cc_start: 0.8890 (pttt) cc_final: 0.8594 (ptmt) REVERT: F 590 GLN cc_start: 0.9381 (mm-40) cc_final: 0.9072 (mm-40) REVERT: F 660 ASN cc_start: 0.8231 (t0) cc_final: 0.7740 (t0) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1416 time to fit residues: 70.9985 Evaluate side-chains 164 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN D 651 ASN A 315 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN F 625 ASN F 640 GLN F 653 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076868 restraints weight = 37703.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078601 restraints weight = 26449.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079874 restraints weight = 20605.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080768 restraints weight = 17126.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.081361 restraints weight = 14929.688| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15320 Z= 0.174 Angle : 0.751 10.892 20988 Z= 0.368 Chirality : 0.047 0.349 2599 Planarity : 0.004 0.036 2560 Dihedral : 7.707 67.120 3380 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.07 % Allowed : 1.65 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.21), residues: 1595 helix: 1.80 (0.29), residues: 359 sheet: 0.41 (0.24), residues: 410 loop : 0.12 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 419 TYR 0.017 0.002 TYR C 40 PHE 0.021 0.002 PHE C 210 TRP 0.020 0.002 TRP C 478 HIS 0.004 0.001 HIS F 570 Details of bonding type rmsd covalent geometry : bond 0.00385 (15218) covalent geometry : angle 0.68874 (20716) SS BOND : bond 0.00291 ( 34) SS BOND : angle 0.82571 ( 68) hydrogen bonds : bond 0.05473 ( 444) hydrogen bonds : angle 5.49961 ( 1176) link_BETA1-4 : bond 0.00455 ( 9) link_BETA1-4 : angle 2.99272 ( 27) link_NAG-ASN : bond 0.00495 ( 59) link_NAG-ASN : angle 3.12143 ( 177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 VAL cc_start: 0.9517 (t) cc_final: 0.9167 (p) REVERT: C 107 ASP cc_start: 0.7949 (t0) cc_final: 0.7731 (t0) REVERT: C 154 MET cc_start: 0.8249 (mmt) cc_final: 0.7538 (mmm) REVERT: C 177 TYR cc_start: 0.8633 (m-80) cc_final: 0.8077 (m-80) REVERT: C 180 ASP cc_start: 0.8890 (m-30) cc_final: 0.8672 (m-30) REVERT: D 586 TYR cc_start: 0.9258 (t80) cc_final: 0.8887 (t80) REVERT: A 112 TRP cc_start: 0.8251 (t-100) cc_final: 0.8005 (t-100) REVERT: A 201 ILE cc_start: 0.9376 (pt) cc_final: 0.9081 (pt) REVERT: A 491 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 596 TRP cc_start: 0.9213 (m-10) cc_final: 0.8929 (m-10) REVERT: B 648 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 657 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7886 (mm-30) REVERT: E 426 MET cc_start: 0.8129 (ttm) cc_final: 0.7748 (ttm) REVERT: E 434 MET cc_start: 0.8129 (ttp) cc_final: 0.7767 (ttp) REVERT: F 588 ARG cc_start: 0.7305 (mpt180) cc_final: 0.6614 (tpt170) REVERT: F 590 GLN cc_start: 0.9251 (mm-40) cc_final: 0.8833 (mm-40) REVERT: F 631 TRP cc_start: 0.9169 (t-100) cc_final: 0.8959 (t-100) REVERT: F 657 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7608 (tp30) REVERT: F 660 ASN cc_start: 0.7709 (t0) cc_final: 0.7090 (t0) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1157 time to fit residues: 40.9143 Evaluate side-chains 156 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 143 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN A 72 HIS ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN B 652 GLN E 428 GLN F 607 ASN F 625 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.072171 restraints weight = 38912.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.073819 restraints weight = 27430.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.074945 restraints weight = 21464.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075783 restraints weight = 18104.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076352 restraints weight = 15887.206| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15320 Z= 0.224 Angle : 0.730 11.736 20988 Z= 0.358 Chirality : 0.047 0.348 2599 Planarity : 0.004 0.038 2560 Dihedral : 6.355 53.096 3380 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.14 % Allowed : 2.19 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.21), residues: 1595 helix: 1.97 (0.28), residues: 354 sheet: 0.12 (0.24), residues: 426 loop : -0.10 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 432 TYR 0.025 0.002 TYR F 638 PHE 0.018 0.002 PHE C 210 TRP 0.017 0.002 TRP B 614 HIS 0.008 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00507 (15218) covalent geometry : angle 0.68129 (20716) SS BOND : bond 0.00629 ( 34) SS BOND : angle 0.78601 ( 68) hydrogen bonds : bond 0.04833 ( 444) hydrogen bonds : angle 5.21381 ( 1176) link_BETA1-4 : bond 0.00599 ( 9) link_BETA1-4 : angle 2.23751 ( 27) link_NAG-ASN : bond 0.00488 ( 59) link_NAG-ASN : angle 2.81052 ( 177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 180 ASP cc_start: 0.8888 (m-30) cc_final: 0.8479 (m-30) REVERT: A 92 ASN cc_start: 0.8123 (m110) cc_final: 0.7823 (m110) REVERT: A 100 MET cc_start: 0.9073 (mtm) cc_final: 0.8843 (mtp) REVERT: A 112 TRP cc_start: 0.8375 (t-100) cc_final: 0.7825 (t-100) REVERT: A 210 PHE cc_start: 0.8736 (m-80) cc_final: 0.8210 (m-10) REVERT: A 432 ARG cc_start: 0.7617 (mtm110) cc_final: 0.6751 (ptp-110) REVERT: B 586 TYR cc_start: 0.9426 (t80) cc_final: 0.9225 (t80) REVERT: B 596 TRP cc_start: 0.9163 (m-10) cc_final: 0.8953 (m-10) REVERT: B 623 TRP cc_start: 0.9374 (m100) cc_final: 0.9074 (m100) REVERT: B 652 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7683 (mt0) REVERT: B 653 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8079 (tm-30) REVERT: E 426 MET cc_start: 0.8129 (ttm) cc_final: 0.7900 (ttm) REVERT: F 588 ARG cc_start: 0.7384 (mmt180) cc_final: 0.6628 (tpt170) REVERT: F 590 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8873 (mm-40) REVERT: F 657 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7593 (tp30) REVERT: F 660 ASN cc_start: 0.7685 (t0) cc_final: 0.7070 (t0) outliers start: 2 outliers final: 0 residues processed: 194 average time/residue: 0.1148 time to fit residues: 33.4622 Evaluate side-chains 138 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 43 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 575 GLN A 72 HIS A 99 ASN A 114 GLN F 591 GLN F 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074214 restraints weight = 38347.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075934 restraints weight = 26986.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077043 restraints weight = 20871.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077922 restraints weight = 17476.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078473 restraints weight = 15320.099| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15320 Z= 0.121 Angle : 0.629 11.736 20988 Z= 0.305 Chirality : 0.044 0.323 2599 Planarity : 0.003 0.034 2560 Dihedral : 5.609 54.303 3380 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.21), residues: 1595 helix: 2.07 (0.28), residues: 354 sheet: 0.17 (0.24), residues: 430 loop : -0.11 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.016 0.001 TYR C 217 PHE 0.016 0.002 PHE C 210 TRP 0.040 0.001 TRP F 614 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00267 (15218) covalent geometry : angle 0.57108 (20716) SS BOND : bond 0.00230 ( 34) SS BOND : angle 0.90113 ( 68) hydrogen bonds : bond 0.04207 ( 444) hydrogen bonds : angle 4.97235 ( 1176) link_BETA1-4 : bond 0.00418 ( 9) link_BETA1-4 : angle 1.85201 ( 27) link_NAG-ASN : bond 0.00335 ( 59) link_NAG-ASN : angle 2.81044 ( 177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 VAL cc_start: 0.9593 (t) cc_final: 0.9322 (p) REVERT: C 180 ASP cc_start: 0.8878 (m-30) cc_final: 0.8494 (m-30) REVERT: D 584 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 112 TRP cc_start: 0.8254 (t-100) cc_final: 0.7989 (t-100) REVERT: B 586 TYR cc_start: 0.9412 (t80) cc_final: 0.9195 (t80) REVERT: B 623 TRP cc_start: 0.9331 (m100) cc_final: 0.9065 (m100) REVERT: B 648 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7163 (tm-30) REVERT: B 653 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8060 (tm-30) REVERT: E 104 MET cc_start: 0.9342 (ttt) cc_final: 0.8984 (ttt) REVERT: F 590 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8927 (mm-40) REVERT: F 657 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7542 (tp30) REVERT: F 660 ASN cc_start: 0.7572 (t0) cc_final: 0.6969 (t0) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1282 time to fit residues: 36.7333 Evaluate side-chains 143 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 152 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 158 optimal weight: 0.9980 chunk 122 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 114 GLN F 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.091985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.073643 restraints weight = 38447.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075289 restraints weight = 27072.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076486 restraints weight = 21163.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077328 restraints weight = 17595.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077873 restraints weight = 15395.870| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.003 0.044 15320 Z= 0.133 Angle : 0.591 11.521 20988 Z= 0.292 Chirality : 0.044 0.320 2599 Planarity : 0.003 0.032 2560 Dihedral : 5.184 53.194 3380 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.21), residues: 1595 helix: 2.26 (0.29), residues: 348 sheet: 0.14 (0.24), residues: 432 loop : -0.10 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 432 TYR 0.017 0.001 TYR D 586 PHE 0.017 0.002 PHE E 375 TRP 0.016 0.001 TRP F 614 HIS 0.005 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00301 (15218) covalent geometry : angle 0.54356 (20716) SS BOND : bond 0.00222 ( 34) SS BOND : angle 0.76772 ( 68) hydrogen bonds : bond 0.03989 ( 444) hydrogen bonds : angle 4.80313 ( 1176) link_BETA1-4 : bond 0.00443 ( 9) link_BETA1-4 : angle 1.53180 ( 27) link_NAG-ASN : bond 0.00371 ( 59) link_NAG-ASN : angle 2.50751 ( 177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 100 MET cc_start: 0.9396 (mtm) cc_final: 0.9181 (mtm) REVERT: C 180 ASP cc_start: 0.8890 (m-30) cc_final: 0.8479 (m-30) REVERT: A 103 GLN cc_start: 0.8213 (tt0) cc_final: 0.7094 (tm-30) REVERT: A 112 TRP cc_start: 0.8270 (t-100) cc_final: 0.8022 (t-100) REVERT: B 623 TRP cc_start: 0.9341 (m100) cc_final: 0.9138 (m100) REVERT: B 648 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7329 (tm-30) REVERT: B 652 GLN cc_start: 0.7804 (mt0) cc_final: 0.7450 (mt0) REVERT: B 653 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8129 (tm-30) REVERT: E 104 MET cc_start: 0.9324 (ttt) cc_final: 0.8969 (ttt) REVERT: E 330 TYR cc_start: 0.8705 (p90) cc_final: 0.8469 (p90) REVERT: F 590 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8920 (mm-40) REVERT: F 601 LYS cc_start: 0.9247 (mttp) cc_final: 0.9011 (mtpt) REVERT: F 660 ASN cc_start: 0.7548 (t0) cc_final: 0.7321 (t0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1170 time to fit residues: 33.4165 Evaluate side-chains 143 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN D 575 GLN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN F 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.091585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.073215 restraints weight = 38256.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.074809 restraints weight = 27015.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075887 restraints weight = 21275.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076788 restraints weight = 17916.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.077336 restraints weight = 15680.547| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15320 Z= 0.145 Angle : 0.597 11.413 20988 Z= 0.293 Chirality : 0.044 0.317 2599 Planarity : 0.003 0.033 2560 Dihedral : 5.158 53.123 3380 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.22), residues: 1595 helix: 2.19 (0.29), residues: 351 sheet: 0.10 (0.24), residues: 440 loop : -0.10 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 166 TYR 0.020 0.001 TYR C 217 PHE 0.014 0.002 PHE C 210 TRP 0.012 0.001 TRP F 614 HIS 0.005 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00332 (15218) covalent geometry : angle 0.54696 (20716) SS BOND : bond 0.00235 ( 34) SS BOND : angle 1.03307 ( 68) hydrogen bonds : bond 0.03964 ( 444) hydrogen bonds : angle 4.78317 ( 1176) link_BETA1-4 : bond 0.00394 ( 9) link_BETA1-4 : angle 1.46600 ( 27) link_NAG-ASN : bond 0.00324 ( 59) link_NAG-ASN : angle 2.54775 ( 177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.8984 (m-30) cc_final: 0.8561 (m-30) REVERT: D 636 SER cc_start: 0.8069 (p) cc_final: 0.7639 (t) REVERT: A 103 GLN cc_start: 0.8245 (tt0) cc_final: 0.7099 (tm-30) REVERT: A 112 TRP cc_start: 0.8266 (t-100) cc_final: 0.8015 (t-100) REVERT: B 584 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6719 (tm-30) REVERT: B 623 TRP cc_start: 0.9350 (m100) cc_final: 0.9122 (m100) REVERT: B 648 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 653 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8216 (tm-30) REVERT: E 94 ASN cc_start: 0.8720 (t0) cc_final: 0.8450 (t0) REVERT: E 104 MET cc_start: 0.9288 (ttt) cc_final: 0.8970 (ttt) REVERT: E 330 TYR cc_start: 0.8647 (p90) cc_final: 0.8399 (p90) REVERT: F 590 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8915 (mm-40) REVERT: F 660 ASN cc_start: 0.7552 (t0) cc_final: 0.7351 (t0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1296 time to fit residues: 36.8488 Evaluate side-chains 148 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 HIS C 463 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.070696 restraints weight = 38568.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072236 restraints weight = 27475.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.073307 restraints weight = 21634.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074125 restraints weight = 18330.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.074627 restraints weight = 16128.230| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 15320 Z= 0.206 Angle : 0.661 11.377 20988 Z= 0.323 Chirality : 0.046 0.331 2599 Planarity : 0.003 0.042 2560 Dihedral : 5.538 51.814 3380 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.21), residues: 1595 helix: 2.16 (0.29), residues: 347 sheet: -0.07 (0.24), residues: 432 loop : -0.25 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 432 TYR 0.022 0.002 TYR D 586 PHE 0.015 0.002 PHE C 375 TRP 0.013 0.002 TRP C 478 HIS 0.010 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00477 (15218) covalent geometry : angle 0.61369 (20716) SS BOND : bond 0.00346 ( 34) SS BOND : angle 1.18070 ( 68) hydrogen bonds : bond 0.04293 ( 444) hydrogen bonds : angle 4.94468 ( 1176) link_BETA1-4 : bond 0.00431 ( 9) link_BETA1-4 : angle 1.53660 ( 27) link_NAG-ASN : bond 0.00370 ( 59) link_NAG-ASN : angle 2.61675 ( 177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.9036 (m-30) cc_final: 0.8509 (m-30) REVERT: D 588 ARG cc_start: 0.8108 (tpt170) cc_final: 0.7701 (tpp-160) REVERT: D 636 SER cc_start: 0.8130 (p) cc_final: 0.7762 (t) REVERT: A 100 MET cc_start: 0.8672 (mtm) cc_final: 0.8450 (mtp) REVERT: A 103 GLN cc_start: 0.8108 (tt0) cc_final: 0.7267 (tm-30) REVERT: A 112 TRP cc_start: 0.8283 (t-100) cc_final: 0.7783 (t-100) REVERT: A 210 PHE cc_start: 0.8875 (m-80) cc_final: 0.8143 (m-80) REVERT: B 653 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8471 (tm-30) REVERT: E 94 ASN cc_start: 0.8731 (t0) cc_final: 0.8475 (t0) REVERT: E 330 TYR cc_start: 0.8653 (p90) cc_final: 0.8406 (p90) REVERT: F 660 ASN cc_start: 0.7687 (t0) cc_final: 0.7240 (t0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1255 time to fit residues: 32.9680 Evaluate side-chains 137 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 89 optimal weight: 0.0030 chunk 56 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 HIS D 575 GLN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN F 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.071435 restraints weight = 38619.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.073007 restraints weight = 27310.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.074045 restraints weight = 21454.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074874 restraints weight = 18172.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075345 restraints weight = 16048.130| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15320 Z= 0.169 Angle : 0.653 11.436 20988 Z= 0.314 Chirality : 0.046 0.594 2599 Planarity : 0.003 0.040 2560 Dihedral : 5.684 52.676 3380 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.22), residues: 1595 helix: 2.06 (0.29), residues: 350 sheet: -0.08 (0.25), residues: 432 loop : -0.24 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 166 TYR 0.019 0.001 TYR D 586 PHE 0.014 0.002 PHE C 375 TRP 0.060 0.002 TRP F 614 HIS 0.007 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00388 (15218) covalent geometry : angle 0.59198 (20716) SS BOND : bond 0.00313 ( 34) SS BOND : angle 1.22284 ( 68) hydrogen bonds : bond 0.04182 ( 444) hydrogen bonds : angle 4.90041 ( 1176) link_BETA1-4 : bond 0.00421 ( 9) link_BETA1-4 : angle 1.36296 ( 27) link_NAG-ASN : bond 0.00382 ( 59) link_NAG-ASN : angle 2.93933 ( 177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.9046 (m-30) cc_final: 0.8516 (m-30) REVERT: A 103 GLN cc_start: 0.8274 (tt0) cc_final: 0.7096 (tm-30) REVERT: A 112 TRP cc_start: 0.8280 (t-100) cc_final: 0.8079 (t-100) REVERT: B 584 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6769 (tm-30) REVERT: B 653 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8590 (tm-30) REVERT: E 94 ASN cc_start: 0.8631 (t0) cc_final: 0.8390 (t0) REVERT: E 104 MET cc_start: 0.9281 (ttt) cc_final: 0.9057 (ttt) REVERT: E 330 TYR cc_start: 0.8602 (p90) cc_final: 0.8344 (p90) REVERT: F 530 MET cc_start: 0.8019 (mtt) cc_final: 0.7096 (mtt) REVERT: F 577 GLN cc_start: 0.8698 (tt0) cc_final: 0.8475 (tt0) REVERT: F 657 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7253 (tp30) REVERT: F 660 ASN cc_start: 0.7632 (t0) cc_final: 0.6879 (t0) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1192 time to fit residues: 31.1548 Evaluate side-chains 142 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.072640 restraints weight = 38505.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074243 restraints weight = 27150.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.075339 restraints weight = 21260.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076004 restraints weight = 17951.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.076643 restraints weight = 15984.735| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15320 Z= 0.124 Angle : 0.604 11.239 20988 Z= 0.294 Chirality : 0.045 0.480 2599 Planarity : 0.003 0.039 2560 Dihedral : 5.335 53.524 3380 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.22), residues: 1595 helix: 2.13 (0.29), residues: 348 sheet: -0.03 (0.25), residues: 442 loop : -0.17 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 432 TYR 0.034 0.001 TYR C 217 PHE 0.015 0.001 PHE C 53 TRP 0.054 0.001 TRP F 614 HIS 0.005 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00279 (15218) covalent geometry : angle 0.54891 (20716) SS BOND : bond 0.00286 ( 34) SS BOND : angle 0.94547 ( 68) hydrogen bonds : bond 0.03895 ( 444) hydrogen bonds : angle 4.80938 ( 1176) link_BETA1-4 : bond 0.00397 ( 9) link_BETA1-4 : angle 1.27017 ( 27) link_NAG-ASN : bond 0.00367 ( 59) link_NAG-ASN : angle 2.71209 ( 177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 MET cc_start: 0.8084 (mmm) cc_final: 0.7867 (mmm) REVERT: C 180 ASP cc_start: 0.8980 (m-30) cc_final: 0.8525 (m-30) REVERT: A 103 GLN cc_start: 0.8220 (tt0) cc_final: 0.7064 (tm-30) REVERT: A 112 TRP cc_start: 0.8283 (t-100) cc_final: 0.7889 (t-100) REVERT: B 584 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6640 (tm-30) REVERT: B 653 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8605 (tm-30) REVERT: E 94 ASN cc_start: 0.8631 (t0) cc_final: 0.7920 (t0) REVERT: E 97 LYS cc_start: 0.8419 (mttp) cc_final: 0.8060 (mttp) REVERT: E 104 MET cc_start: 0.9259 (ttt) cc_final: 0.8981 (ttt) REVERT: E 330 TYR cc_start: 0.8567 (p90) cc_final: 0.8311 (p90) REVERT: F 530 MET cc_start: 0.8028 (mtt) cc_final: 0.7276 (mtt) REVERT: F 577 GLN cc_start: 0.8698 (tt0) cc_final: 0.8494 (tt0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1124 time to fit residues: 30.1138 Evaluate side-chains 143 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 75 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 125 optimal weight: 0.0020 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 69 optimal weight: 0.0980 chunk 129 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 HIS D 575 GLN D 651 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN A 425 ASN F 591 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074055 restraints weight = 38340.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075645 restraints weight = 27001.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.076771 restraints weight = 21201.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.077506 restraints weight = 17796.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078112 restraints weight = 15744.649| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15320 Z= 0.105 Angle : 0.593 12.412 20988 Z= 0.288 Chirality : 0.045 0.349 2599 Planarity : 0.003 0.043 2560 Dihedral : 5.153 54.312 3380 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.07 % Allowed : 0.00 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.22), residues: 1595 helix: 2.26 (0.29), residues: 341 sheet: -0.01 (0.24), residues: 447 loop : -0.15 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.018 0.001 TYR D 586 PHE 0.016 0.001 PHE C 375 TRP 0.050 0.001 TRP F 614 HIS 0.004 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00230 (15218) covalent geometry : angle 0.53343 (20716) SS BOND : bond 0.00181 ( 34) SS BOND : angle 1.10596 ( 68) hydrogen bonds : bond 0.03667 ( 444) hydrogen bonds : angle 4.68720 ( 1176) link_BETA1-4 : bond 0.00425 ( 9) link_BETA1-4 : angle 1.23314 ( 27) link_NAG-ASN : bond 0.00403 ( 59) link_NAG-ASN : angle 2.77329 ( 177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.8967 (m-30) cc_final: 0.8509 (m-30) REVERT: D 586 TYR cc_start: 0.9206 (t80) cc_final: 0.8992 (t80) REVERT: D 632 ASP cc_start: 0.9056 (t70) cc_final: 0.8824 (t0) REVERT: A 103 GLN cc_start: 0.8129 (tt0) cc_final: 0.6943 (tm-30) REVERT: A 112 TRP cc_start: 0.8216 (t-100) cc_final: 0.7900 (t-100) REVERT: B 584 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6650 (tm-30) REVERT: B 653 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8571 (tm-30) REVERT: E 94 ASN cc_start: 0.8498 (t0) cc_final: 0.7698 (t0) REVERT: E 97 LYS cc_start: 0.8389 (mttp) cc_final: 0.7993 (mttp) REVERT: E 104 MET cc_start: 0.9247 (ttt) cc_final: 0.8981 (ttt) REVERT: E 330 TYR cc_start: 0.8518 (p90) cc_final: 0.8268 (p90) REVERT: F 530 MET cc_start: 0.7758 (mtt) cc_final: 0.7095 (mtt) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1234 time to fit residues: 35.4280 Evaluate side-chains 157 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 HIS C 373 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN F 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.091316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.073202 restraints weight = 38276.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074716 restraints weight = 27209.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075733 restraints weight = 21432.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.076524 restraints weight = 18178.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077024 restraints weight = 16084.799| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15320 Z= 0.144 Angle : 0.610 10.867 20988 Z= 0.297 Chirality : 0.045 0.314 2599 Planarity : 0.003 0.047 2560 Dihedral : 5.202 53.047 3380 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.22), residues: 1595 helix: 1.94 (0.29), residues: 355 sheet: -0.01 (0.25), residues: 442 loop : -0.18 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 432 TYR 0.011 0.001 TYR D 586 PHE 0.014 0.002 PHE C 375 TRP 0.048 0.001 TRP F 614 HIS 0.009 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00331 (15218) covalent geometry : angle 0.55917 (20716) SS BOND : bond 0.00275 ( 34) SS BOND : angle 1.09391 ( 68) hydrogen bonds : bond 0.03836 ( 444) hydrogen bonds : angle 4.70601 ( 1176) link_BETA1-4 : bond 0.00386 ( 9) link_BETA1-4 : angle 1.28638 ( 27) link_NAG-ASN : bond 0.00340 ( 59) link_NAG-ASN : angle 2.59910 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.38 seconds wall clock time: 40 minutes 45.28 seconds (2445.28 seconds total)