Starting phenix.real_space_refine on Sat Sep 12 13:00:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8w_23238/09_2026/7l8w_23238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8w_23238/09_2026/7l8w_23238.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 { model { file = "/net/cci-nas-00/data/ceres_data/7l8w_23238/09_2026/7l8w_23238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8w_23238/09_2026/7l8w_23238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8w_23238/09_2026/7l8w_23238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8w_23238/09_2026/7l8w_23238.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l8w_23238/09_2026/7l8w_23238.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8w_23238/09_2026/7l8w_23238.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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 105 5.16 5 C 9845 2.51 5 N 2677 2.21 5 O 3176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15803 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3485 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1055 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3460 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1060 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3466 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'UNK:plan-1': 103} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "M" 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 chiralities: 2 Chain: "N" 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 chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "P" 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 chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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 chiralities: 16 Chain: "D" 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 chiralities: 3 Chain: "E" 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 chiralities: 16 Chain: "F" 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 chiralities: 3 Time building chain proxies: 2.78, per 1000 atoms: 0.18 Number of scatterers: 15803 At special positions: 0 Unit cell: (127.72, 136.99, 118.45, 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 105 16.00 O 3176 8.00 N 2677 7.00 C 9845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 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=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.10 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 8 " " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 9 " " BMA K 3 " - " MAN K 5 " " BMA O 3 " - " MAN O 5 " 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 386 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 160 " " NAG A 613 " - " ASN A 197 " " NAG A 614 " - " ASN A 133 " " NAG A 615 " - " ASN A 289 " " NAG A 616 " - " ASN A 137 " " NAG A 617 " - " ASN A 363 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 197 " " NAG C 613 " - " ASN C 133 " " NAG C 614 " - " ASN C 355 " " NAG C 615 " - " ASN C 289 " " NAG C 616 " - " ASN C 363 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 386 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 160 " " NAG E 612 " - " ASN E 197 " " NAG E 613 " - " ASN E 133 " " NAG E 614 " - " ASN E 355 " " NAG E 615 " - " ASN E 289 " " NAG E 616 " - " ASN E 363 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN C 332 " " NAG K 1 " - " ASN C 262 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN E 332 " " NAG O 1 " - " ASN E 262 " " NAG P 1 " - " ASN E 156 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 587.4 milliseconds 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 32 sheets defined 31.7% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.525A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.534A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 558 through 568 removed outlier: 3.744A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 661 removed outlier: 3.631A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.504A 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 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.783A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.345A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 544 removed outlier: 4.084A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.965A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.015A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.762A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.500A pdb=" N ARG E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.117A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 545 removed outlier: 4.027A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.687A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.648A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.264A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.445A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.334A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.678A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.880A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 3.753A pdb=" N ILE C 309 " --> pdb=" O GLN C 315 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.351A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.704A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.236A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.698A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.522A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 3.783A pdb=" N ILE E 309 " --> pdb=" O GLN E 315 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.778A pdb=" N UNK H 18 " --> pdb=" O UNK H 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 56 through 58 Processing sheet with id=AD3, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AD4, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.561A pdb=" N UNK L 37 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK L 86 " --> pdb=" O UNK L 40 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1797 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: 1.98 Time building geometry restraints manager: 1.73 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: 3102 1.32 - 1.46: 5297 1.46 - 1.60: 7510 1.60 - 1.74: 30 1.74 - 1.88: 133 Bond restraints: 16072 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.414 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.36e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 4.98e+01 bond pdb=" NE ARG C 550 " pdb=" CZ ARG C 550 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.74e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 16067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 18523 2.29 - 4.58: 2814 4.58 - 6.87: 469 6.87 - 9.16: 44 9.16 - 11.44: 2 Bond angle restraints: 21852 Sorted by residual: angle pdb=" C PHE C 53 " pdb=" N CYS C 54 " pdb=" CA CYS C 54 " ideal model delta sigma weight residual 122.19 133.63 -11.44 1.41e+00 5.03e-01 6.59e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.67 -8.11 1.01e+00 9.80e-01 6.44e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.47 103.05 7.42 9.60e-01 1.09e+00 5.98e+01 angle pdb=" N THR A 464 " pdb=" CA THR A 464 " pdb=" C THR A 464 " ideal model delta sigma weight residual 113.23 122.33 -9.10 1.24e+00 6.50e-01 5.39e+01 angle pdb=" C CYS C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.56 126.89 -7.33 1.02e+00 9.61e-01 5.16e+01 ... (remaining 21847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 8678 17.16 - 34.33: 245 34.33 - 51.49: 73 51.49 - 68.65: 30 68.65 - 85.82: 12 Dihedral angle restraints: 9038 sinusoidal: 3449 harmonic: 5589 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.12 -73.12 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 164.19 -71.19 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.81 -66.81 1 1.00e+01 1.00e-02 5.82e+01 ... (remaining 9035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 2395 0.188 - 0.376: 311 0.376 - 0.565: 64 0.565 - 0.753: 1 0.753 - 0.941: 2 Chirality restraints: 2773 Sorted by residual: chirality pdb=" C1 MAN G 8 " pdb=" O3 MAN G 7 " pdb=" C2 MAN G 8 " pdb=" O5 MAN G 8 " both_signs ideal model delta sigma weight residual False 2.40 1.46 0.94 2.00e-02 2.50e+03 2.21e+03 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 1.07e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.53e+01 ... (remaining 2770 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " -0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 602 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.332 2.00e-02 2.50e+03 2.83e-01 9.99e+02 pdb=" C7 NAG A 607 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.496 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 612 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.39e+02 pdb=" C7 NAG A 612 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 612 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A 612 " -0.479 2.00e-02 2.50e+03 pdb=" O7 NAG A 612 " 0.060 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5748 2.88 - 3.39: 14373 3.39 - 3.89: 25518 3.89 - 4.40: 29106 4.40 - 4.90: 45961 Nonbonded interactions: 120706 Sorted by model distance: nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.378 2.496 nonbonded pdb=" O3 NAG D 703 " pdb=" O7 NAG D 703 " model vdw 2.383 3.040 nonbonded pdb=" O ASN A 80 " pdb=" NE2 GLN A 82 " model vdw 2.436 3.120 nonbonded pdb=" OD1 ASN E 234 " pdb=" N GLY E 235 " model vdw 2.451 3.120 nonbonded pdb=" N ASP C 167 " pdb=" OD1 ASP C 167 " model vdw 2.488 3.120 ... (remaining 120701 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 57 or resid 64 through 616)) selection = (chain 'C' and (resid 33 through 185 or resid 189 through 457 or resid 461 throu \ gh 616)) selection = (chain 'E' and (resid 33 through 57 or resid 64 through 457 or resid 461 through \ 616)) } ncs_group { reference = (chain 'B' and (resid 521 through 546 or resid 558 through 702)) selection = (chain 'D' and (resid 521 through 662 or resid 702 through 703)) selection = (chain 'F' and (resid 521 through 662 or resid 702 through 703)) } ncs_group { reference = (chain 'H' and resid 8 through 110) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'O' } 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: 3.260 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 0.121 16194 Z= 1.163 Angle : 1.742 11.444 22182 Z= 1.105 Chirality : 0.137 0.941 2773 Planarity : 0.018 0.291 2679 Dihedral : 10.044 85.817 5290 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 are not related in a simple way. whole: 1.14 (0.19), residues: 1678 helix: 0.58 (0.22), residues: 427 sheet: 1.21 (0.23), residues: 465 loop : 0.77 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 542 TYR 0.071 0.008 TYR D 638 PHE 0.039 0.006 PHE A 383 TRP 0.074 0.010 TRP C 35 HIS 0.013 0.002 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.02121 / 1.14 (16072) covalent geometry : angle 1.70907 / 1.10 (21852) SS BOND : bond 0.02180 / 1.22 ( 36) SS BOND : angle 3.11253 / 2.15 ( 72) hydrogen bonds : bond 0.17631 / 11.69 ( 650) hydrogen bonds : angle 7.37557 / 5.12 ( 1797) link_ALPHA1-2 : bond 0.05982 / 2.87 ( 2) link_ALPHA1-2 : angle 4.07674 / 2.92 ( 6) link_ALPHA1-3 : bond 0.06061 / 3.04 ( 4) link_ALPHA1-3 : angle 5.03794 / 3.39 ( 12) link_ALPHA1-6 : bond 0.05963 / 2.98 ( 4) link_ALPHA1-6 : angle 3.37177 / 1.87 ( 12) link_BETA1-4 : bond 0.05895 / 3.74 ( 11) link_BETA1-4 : angle 3.99102 / 2.43 ( 33) link_NAG-ASN : bond 0.07109 / 4.43 ( 65) link_NAG-ASN : angle 2.98335 / 2.08 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9435 (p) cc_final: 0.8935 (t) REVERT: A 257 THR cc_start: 0.8957 (p) cc_final: 0.8658 (m) REVERT: B 591 GLN cc_start: 0.9098 (tt0) cc_final: 0.8843 (tt0) REVERT: B 599 SER cc_start: 0.9019 (p) cc_final: 0.8335 (t) REVERT: B 601 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8606 (tptp) REVERT: C 38 VAL cc_start: 0.8541 (t) cc_final: 0.8179 (t) REVERT: C 69 TRP cc_start: 0.8141 (m-10) cc_final: 0.7906 (m-10) REVERT: C 102 GLU cc_start: 0.8251 (tp30) cc_final: 0.7745 (tm-30) REVERT: C 199 SER cc_start: 0.9546 (p) cc_final: 0.9296 (t) REVERT: D 585 ARG cc_start: 0.9197 (mmt180) cc_final: 0.8898 (ttm-80) REVERT: D 586 TYR cc_start: 0.9636 (t80) cc_final: 0.9356 (t80) REVERT: D 623 TRP cc_start: 0.8861 (m100) cc_final: 0.8398 (m-10) REVERT: E 45 TRP cc_start: 0.8802 (p90) cc_final: 0.8589 (p90) REVERT: E 57 ASP cc_start: 0.8224 (t0) cc_final: 0.7884 (p0) REVERT: E 103 GLN cc_start: 0.8566 (tt0) cc_final: 0.8206 (tm-30) REVERT: E 381 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7551 (tt0) REVERT: F 579 ARG cc_start: 0.9118 (mtp180) cc_final: 0.8780 (ttm170) REVERT: F 629 LEU cc_start: 0.9059 (tp) cc_final: 0.8765 (mp) REVERT: F 638 TYR cc_start: 0.8320 (m-80) cc_final: 0.8067 (m-10) REVERT: F 650 GLN cc_start: 0.8917 (tp40) cc_final: 0.7736 (tm-30) REVERT: F 654 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7132 (mt-10) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.1334 time to fit residues: 98.2242 Evaluate side-chains 248 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 422 GLN C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 203 GLN E 287 GLN E 300 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093772 restraints weight = 35298.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096480 restraints weight = 20911.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098306 restraints weight = 14679.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099459 restraints weight = 11502.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100370 restraints weight = 9779.379| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16194 Z= 0.186 Angle : 0.852 15.780 22182 Z= 0.408 Chirality : 0.052 0.636 2773 Planarity : 0.004 0.042 2679 Dihedral : 5.071 26.728 2025 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.07 % Favored : 98.87 % Rotamer: Outliers : 0.33 % Allowed : 2.42 % Favored : 97.25 % 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 are not related in a simple way. whole: 1.17 (0.20), residues: 1678 helix: 1.87 (0.25), residues: 426 sheet: 1.01 (0.23), residues: 443 loop : 0.12 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 151 TYR 0.017 0.002 TYR B 643 PHE 0.020 0.002 PHE A 383 TRP 0.027 0.002 TRP A 69 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (16072) covalent geometry : angle 0.78169 / 0.39 (21852) SS BOND : bond 0.00267 / 0.19 ( 36) SS BOND : angle 1.41238 / 1.06 ( 72) hydrogen bonds : bond 0.06254 / 4.14 ( 650) hydrogen bonds : angle 6.09679 / 4.25 ( 1797) link_ALPHA1-2 : bond 0.01015 / 0.52 ( 2) link_ALPHA1-2 : angle 1.99068 / 1.36 ( 6) link_ALPHA1-3 : bond 0.01357 / 0.66 ( 4) link_ALPHA1-3 : angle 2.26016 / 1.68 ( 12) link_ALPHA1-6 : bond 0.01017 / 0.49 ( 4) link_ALPHA1-6 : angle 1.71865 / 1.39 ( 12) link_BETA1-4 : bond 0.00996 / 0.64 ( 11) link_BETA1-4 : angle 2.68362 / 1.58 ( 33) link_NAG-ASN : bond 0.00630 / 0.40 ( 65) link_NAG-ASN : angle 3.39398 / 2.30 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 365 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ILE cc_start: 0.9273 (mm) cc_final: 0.9060 (mm) REVERT: A 209 SER cc_start: 0.8497 (t) cc_final: 0.8038 (p) REVERT: A 475 MET cc_start: 0.8829 (mmm) cc_final: 0.8608 (mmm) REVERT: B 568 LEU cc_start: 0.8443 (mp) cc_final: 0.8193 (mp) REVERT: B 602 LEU cc_start: 0.8740 (mt) cc_final: 0.8393 (pt) REVERT: B 641 ILE cc_start: 0.8004 (mp) cc_final: 0.7283 (tp) REVERT: B 643 TYR cc_start: 0.9042 (m-10) cc_final: 0.8784 (m-10) REVERT: C 38 VAL cc_start: 0.8461 (t) cc_final: 0.7862 (t) REVERT: C 104 MET cc_start: 0.8611 (ttt) cc_final: 0.8229 (ttt) REVERT: C 114 GLN cc_start: 0.8448 (tp40) cc_final: 0.7543 (tm-30) REVERT: C 199 SER cc_start: 0.9461 (p) cc_final: 0.9162 (t) REVERT: C 286 VAL cc_start: 0.9297 (t) cc_final: 0.9079 (m) REVERT: C 377 ASN cc_start: 0.9156 (t0) cc_final: 0.8751 (t0) REVERT: C 395 TRP cc_start: 0.7669 (m100) cc_final: 0.7443 (m100) REVERT: C 486 TYR cc_start: 0.9058 (m-80) cc_final: 0.8771 (m-80) REVERT: D 565 LEU cc_start: 0.7882 (tp) cc_final: 0.7368 (tp) REVERT: D 577 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7735 (tm-30) REVERT: D 643 TYR cc_start: 0.8939 (m-10) cc_final: 0.8661 (m-80) REVERT: E 51 THR cc_start: 0.9052 (m) cc_final: 0.8651 (p) REVERT: E 103 GLN cc_start: 0.8139 (tt0) cc_final: 0.7686 (tm-30) REVERT: E 434 MET cc_start: 0.8746 (tmm) cc_final: 0.8545 (ttp) REVERT: F 543 ASN cc_start: 0.8501 (t0) cc_final: 0.8194 (t0) REVERT: F 590 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8942 (tp40) REVERT: F 629 LEU cc_start: 0.8897 (tp) cc_final: 0.8159 (pp) REVERT: F 631 TRP cc_start: 0.7946 (t60) cc_final: 0.7517 (t60) REVERT: F 634 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8137 (mm-30) REVERT: F 648 GLU cc_start: 0.8327 (tp30) cc_final: 0.8071 (tp30) REVERT: F 650 GLN cc_start: 0.8925 (tp40) cc_final: 0.8371 (tm-30) REVERT: F 652 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8277 (tt0) REVERT: F 653 GLN cc_start: 0.8300 (tt0) cc_final: 0.8064 (tt0) outliers start: 5 outliers final: 2 residues processed: 368 average time/residue: 0.1205 time to fit residues: 65.8189 Evaluate side-chains 245 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 121 optimal weight: 0.0670 chunk 140 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 59.3808 > 50:) chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS B 562 GLN B 658 GLN C 302 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.088701 restraints weight = 36163.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.091278 restraints weight = 21719.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093031 restraints weight = 15403.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094217 restraints weight = 12185.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094942 restraints weight = 10356.785| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16194 Z= 0.235 Angle : 0.805 13.184 22182 Z= 0.388 Chirality : 0.050 0.502 2773 Planarity : 0.004 0.042 2679 Dihedral : 5.014 28.416 2025 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.85 % Favored : 98.09 % Rotamer: Outliers : 0.13 % Allowed : 3.08 % Favored : 96.79 % 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 are not related in a simple way. whole: 0.92 (0.20), residues: 1678 helix: 1.70 (0.25), residues: 428 sheet: 0.87 (0.24), residues: 430 loop : -0.04 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 617 TYR 0.016 0.002 TYR E 173 PHE 0.019 0.002 PHE A 383 TRP 0.028 0.002 TRP D 571 HIS 0.005 0.001 HIS F 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (16072) covalent geometry : angle 0.74888 / 0.38 (21852) SS BOND : bond 0.00514 / 0.36 ( 36) SS BOND : angle 1.57128 / 1.13 ( 72) hydrogen bonds : bond 0.05563 / 3.72 ( 650) hydrogen bonds : angle 5.79115 / 4.05 ( 1797) link_ALPHA1-2 : bond 0.00602 / 0.30 ( 2) link_ALPHA1-2 : angle 2.05140 / 1.77 ( 6) link_ALPHA1-3 : bond 0.01121 / 0.54 ( 4) link_ALPHA1-3 : angle 2.16875 / 1.64 ( 12) link_ALPHA1-6 : bond 0.01010 / 0.50 ( 4) link_ALPHA1-6 : angle 1.63662 / 1.29 ( 12) link_BETA1-4 : bond 0.00649 / 0.43 ( 11) link_BETA1-4 : angle 2.06355 / 1.24 ( 33) link_NAG-ASN : bond 0.00504 / 0.29 ( 65) link_NAG-ASN : angle 2.93258 / 1.99 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.8430 (m) cc_final: 0.7733 (p) REVERT: A 101 VAL cc_start: 0.9320 (m) cc_final: 0.9022 (p) REVERT: A 209 SER cc_start: 0.8714 (t) cc_final: 0.8447 (p) REVERT: A 256 SER cc_start: 0.9497 (p) cc_final: 0.9052 (m) REVERT: A 475 MET cc_start: 0.8912 (mmm) cc_final: 0.8651 (mmm) REVERT: B 599 SER cc_start: 0.8906 (p) cc_final: 0.8207 (t) REVERT: B 603 ILE cc_start: 0.8248 (mm) cc_final: 0.8020 (tt) REVERT: B 634 GLU cc_start: 0.7775 (pt0) cc_final: 0.7286 (pp20) REVERT: B 641 ILE cc_start: 0.8019 (mp) cc_final: 0.7527 (tp) REVERT: B 643 TYR cc_start: 0.9140 (m-10) cc_final: 0.8854 (m-10) REVERT: C 38 VAL cc_start: 0.8343 (t) cc_final: 0.7934 (t) REVERT: C 199 SER cc_start: 0.9466 (p) cc_final: 0.9161 (t) REVERT: C 323 ILE cc_start: 0.8219 (mt) cc_final: 0.8001 (mt) REVERT: C 377 ASN cc_start: 0.9247 (t0) cc_final: 0.8857 (t0) REVERT: C 395 TRP cc_start: 0.7578 (m100) cc_final: 0.7287 (m100) REVERT: C 414 ILE cc_start: 0.9377 (mm) cc_final: 0.9158 (tp) REVERT: C 475 MET cc_start: 0.8504 (mmm) cc_final: 0.7959 (mmm) REVERT: D 565 LEU cc_start: 0.7807 (tp) cc_final: 0.7569 (tp) REVERT: D 571 TRP cc_start: 0.7240 (t60) cc_final: 0.6887 (t60) REVERT: D 577 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7886 (tm-30) REVERT: E 103 GLN cc_start: 0.8250 (tt0) cc_final: 0.7949 (tm-30) REVERT: F 536 THR cc_start: 0.8250 (p) cc_final: 0.8043 (p) REVERT: F 607 ASN cc_start: 0.8892 (p0) cc_final: 0.8459 (p0) REVERT: F 629 LEU cc_start: 0.8681 (tp) cc_final: 0.8423 (tp) REVERT: F 634 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8122 (mm-30) REVERT: F 648 GLU cc_start: 0.8395 (tp30) cc_final: 0.8147 (tp30) outliers start: 2 outliers final: 0 residues processed: 303 average time/residue: 0.1222 time to fit residues: 54.8500 Evaluate side-chains 230 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 171 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 249 HIS E 428 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091061 restraints weight = 35791.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093690 restraints weight = 21184.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095462 restraints weight = 14920.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096549 restraints weight = 11766.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097472 restraints weight = 10050.482| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16194 Z= 0.143 Angle : 0.695 11.572 22182 Z= 0.332 Chirality : 0.046 0.422 2773 Planarity : 0.003 0.039 2679 Dihedral : 4.766 26.380 2025 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Rotamer: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % 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 are not related in a simple way. whole: 0.94 (0.20), residues: 1678 helix: 1.91 (0.25), residues: 428 sheet: 0.80 (0.23), residues: 447 loop : -0.13 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.024 0.001 TYR D 643 PHE 0.014 0.002 PHE A 383 TRP 0.034 0.002 TRP C 69 HIS 0.004 0.001 HIS F 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16072) covalent geometry : angle 0.64378 / 0.32 (21852) SS BOND : bond 0.00313 / 0.19 ( 36) SS BOND : angle 1.43572 / 1.11 ( 72) hydrogen bonds : bond 0.04628 / 3.09 ( 650) hydrogen bonds : angle 5.48474 / 3.83 ( 1797) link_ALPHA1-2 : bond 0.00913 / 0.46 ( 2) link_ALPHA1-2 : angle 1.74447 / 1.39 ( 6) link_ALPHA1-3 : bond 0.01295 / 0.63 ( 4) link_ALPHA1-3 : angle 2.03877 / 1.52 ( 12) link_ALPHA1-6 : bond 0.00954 / 0.47 ( 4) link_ALPHA1-6 : angle 1.56927 / 1.21 ( 12) link_BETA1-4 : bond 0.00676 / 0.42 ( 11) link_BETA1-4 : angle 1.70640 / 1.03 ( 33) link_NAG-ASN : bond 0.00411 / 0.28 ( 65) link_NAG-ASN : angle 2.59074 / 1.75 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 THR cc_start: 0.8164 (m) cc_final: 0.7666 (p) REVERT: A 101 VAL cc_start: 0.9264 (m) cc_final: 0.8939 (p) REVERT: A 104 MET cc_start: 0.9020 (tpp) cc_final: 0.8688 (tpp) REVERT: A 209 SER cc_start: 0.8738 (t) cc_final: 0.8476 (p) REVERT: A 256 SER cc_start: 0.9426 (p) cc_final: 0.8940 (m) REVERT: B 560 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7965 (mm-30) REVERT: B 599 SER cc_start: 0.8916 (p) cc_final: 0.8254 (t) REVERT: B 603 ILE cc_start: 0.8192 (mm) cc_final: 0.7901 (tt) REVERT: B 641 ILE cc_start: 0.8025 (mp) cc_final: 0.7545 (tp) REVERT: B 643 TYR cc_start: 0.9071 (m-10) cc_final: 0.8813 (m-10) REVERT: C 38 VAL cc_start: 0.8080 (t) cc_final: 0.7601 (t) REVERT: C 199 SER cc_start: 0.9432 (p) cc_final: 0.9125 (t) REVERT: C 286 VAL cc_start: 0.9293 (t) cc_final: 0.9047 (m) REVERT: C 377 ASN cc_start: 0.9210 (t0) cc_final: 0.8758 (t0) REVERT: C 414 ILE cc_start: 0.9344 (mm) cc_final: 0.9117 (tp) REVERT: C 434 MET cc_start: 0.8957 (ttp) cc_final: 0.8692 (mtp) REVERT: D 577 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7759 (tm-30) REVERT: D 586 TYR cc_start: 0.9313 (t80) cc_final: 0.9075 (t80) REVERT: D 601 LYS cc_start: 0.9129 (ptpt) cc_final: 0.8762 (ptpp) REVERT: D 615 SER cc_start: 0.8268 (t) cc_final: 0.7954 (m) REVERT: D 650 GLN cc_start: 0.8724 (tp40) cc_final: 0.7867 (tm-30) REVERT: E 103 GLN cc_start: 0.8115 (tt0) cc_final: 0.7850 (tm-30) REVERT: E 150 MET cc_start: 0.7983 (mmm) cc_final: 0.7406 (mmt) REVERT: E 256 SER cc_start: 0.9471 (p) cc_final: 0.9266 (m) REVERT: E 381 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6948 (tt0) REVERT: F 607 ASN cc_start: 0.8875 (p0) cc_final: 0.8365 (p0) REVERT: F 631 TRP cc_start: 0.8208 (t60) cc_final: 0.8007 (t60) REVERT: F 634 GLU cc_start: 0.8718 (mt-10) cc_final: 0.7960 (mm-30) REVERT: F 648 GLU cc_start: 0.8334 (tp30) cc_final: 0.8095 (tp30) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.1224 time to fit residues: 56.5373 Evaluate side-chains 241 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN B 540 GLN B 562 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 258 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.102909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.084172 restraints weight = 36449.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.086497 restraints weight = 22444.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088042 restraints weight = 16222.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089145 restraints weight = 13051.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089809 restraints weight = 11202.117| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 16194 Z= 0.289 Angle : 0.848 14.362 22182 Z= 0.405 Chirality : 0.050 0.394 2773 Planarity : 0.005 0.057 2679 Dihedral : 5.098 23.506 2025 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.05 % 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 are not related in a simple way. whole: 0.53 (0.20), residues: 1678 helix: 1.62 (0.25), residues: 422 sheet: 0.51 (0.24), residues: 432 loop : -0.35 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 151 TYR 0.018 0.002 TYR E 173 PHE 0.022 0.003 PHE A 93 TRP 0.046 0.002 TRP C 69 HIS 0.007 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 (16072) covalent geometry : angle 0.79144 / 0.39 (21852) SS BOND : bond 0.00698 / 0.54 ( 36) SS BOND : angle 1.75790 / 1.26 ( 72) hydrogen bonds : bond 0.05346 / 3.59 ( 650) hydrogen bonds : angle 5.65406 / 3.98 ( 1797) link_ALPHA1-2 : bond 0.00502 / 0.26 ( 2) link_ALPHA1-2 : angle 1.99987 / 1.72 ( 6) link_ALPHA1-3 : bond 0.00952 / 0.46 ( 4) link_ALPHA1-3 : angle 2.27430 / 1.60 ( 12) link_ALPHA1-6 : bond 0.01020 / 0.50 ( 4) link_ALPHA1-6 : angle 1.80547 / 1.40 ( 12) link_BETA1-4 : bond 0.00414 / 0.29 ( 11) link_BETA1-4 : angle 1.84909 / 1.10 ( 33) link_NAG-ASN : bond 0.00517 / 0.30 ( 65) link_NAG-ASN : angle 3.05129 / 2.07 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8905 (t) cc_final: 0.8689 (p) REVERT: A 217 TYR cc_start: 0.8482 (m-10) cc_final: 0.8246 (m-10) REVERT: A 256 SER cc_start: 0.9500 (p) cc_final: 0.9024 (m) REVERT: A 315 GLN cc_start: 0.8527 (mp10) cc_final: 0.8285 (mp10) REVERT: A 475 MET cc_start: 0.8880 (mmm) cc_final: 0.8612 (mmm) REVERT: B 599 SER cc_start: 0.8992 (p) cc_final: 0.8401 (t) REVERT: B 641 ILE cc_start: 0.8059 (mp) cc_final: 0.7609 (tp) REVERT: B 643 TYR cc_start: 0.9149 (m-10) cc_final: 0.8878 (m-10) REVERT: C 38 VAL cc_start: 0.8319 (t) cc_final: 0.8094 (t) REVERT: C 98 ASN cc_start: 0.9143 (t0) cc_final: 0.8820 (t0) REVERT: C 150 MET cc_start: 0.8774 (ppp) cc_final: 0.7849 (ppp) REVERT: C 199 SER cc_start: 0.9454 (p) cc_final: 0.9135 (t) REVERT: C 475 MET cc_start: 0.8767 (mmm) cc_final: 0.8319 (mmm) REVERT: D 565 LEU cc_start: 0.8051 (tp) cc_final: 0.7465 (tp) REVERT: D 571 TRP cc_start: 0.7385 (t60) cc_final: 0.6947 (t60) REVERT: D 601 LYS cc_start: 0.9217 (ptpt) cc_final: 0.8844 (ptpp) REVERT: D 610 TRP cc_start: 0.7956 (t-100) cc_final: 0.7755 (t-100) REVERT: E 103 GLN cc_start: 0.8511 (tt0) cc_final: 0.7894 (tm-30) REVERT: E 150 MET cc_start: 0.8030 (mmm) cc_final: 0.7618 (mmt) REVERT: E 381 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7064 (tt0) REVERT: F 543 ASN cc_start: 0.8614 (t0) cc_final: 0.8317 (t0) REVERT: F 607 ASN cc_start: 0.9096 (p0) cc_final: 0.8471 (p0) REVERT: F 626 MET cc_start: 0.7507 (ttm) cc_final: 0.7121 (ttm) REVERT: F 634 GLU cc_start: 0.8771 (mt-10) cc_final: 0.7970 (mm-30) REVERT: F 648 GLU cc_start: 0.8456 (tp30) cc_final: 0.8231 (tp30) outliers start: 2 outliers final: 0 residues processed: 269 average time/residue: 0.1139 time to fit residues: 45.6187 Evaluate side-chains 209 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 71 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 182 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 133 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.3848 > 50:) chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS F 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.086057 restraints weight = 35904.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088446 restraints weight = 21703.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090080 restraints weight = 15470.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.091197 restraints weight = 12239.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091855 restraints weight = 10383.559| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 16194 Z= 0.178 Angle : 0.737 14.212 22182 Z= 0.350 Chirality : 0.048 0.445 2773 Planarity : 0.004 0.046 2679 Dihedral : 4.857 25.011 2025 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 are not related in a simple way. whole: 0.56 (0.20), residues: 1678 helix: 1.79 (0.26), residues: 422 sheet: 0.54 (0.24), residues: 435 loop : -0.43 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 308 TYR 0.016 0.002 TYR E 173 PHE 0.015 0.002 PHE C 93 TRP 0.049 0.002 TRP C 69 HIS 0.006 0.001 HIS D 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (16072) covalent geometry : angle 0.67887 / 0.34 (21852) SS BOND : bond 0.00414 / 0.29 ( 36) SS BOND : angle 1.55681 / 1.16 ( 72) hydrogen bonds : bond 0.04771 / 3.20 ( 650) hydrogen bonds : angle 5.42334 / 3.81 ( 1797) link_ALPHA1-2 : bond 0.00697 / 0.36 ( 2) link_ALPHA1-2 : angle 1.75471 / 1.47 ( 6) link_ALPHA1-3 : bond 0.01104 / 0.53 ( 4) link_ALPHA1-3 : angle 2.11825 / 1.50 ( 12) link_ALPHA1-6 : bond 0.00914 / 0.45 ( 4) link_ALPHA1-6 : angle 1.59553 / 1.21 ( 12) link_BETA1-4 : bond 0.00450 / 0.30 ( 11) link_BETA1-4 : angle 1.51252 / 0.92 ( 33) link_NAG-ASN : bond 0.00377 / 0.23 ( 65) link_NAG-ASN : angle 2.89182 / 1.97 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9171 (tpp) cc_final: 0.8792 (tpp) REVERT: A 202 THR cc_start: 0.9563 (m) cc_final: 0.9203 (p) REVERT: A 256 SER cc_start: 0.9413 (p) cc_final: 0.9027 (m) REVERT: A 315 GLN cc_start: 0.8611 (mp10) cc_final: 0.8400 (mp10) REVERT: B 560 GLU cc_start: 0.7779 (mp0) cc_final: 0.7560 (mm-30) REVERT: B 599 SER cc_start: 0.8937 (p) cc_final: 0.8373 (t) REVERT: B 641 ILE cc_start: 0.8063 (mp) cc_final: 0.7599 (tp) REVERT: B 643 TYR cc_start: 0.9111 (m-10) cc_final: 0.8834 (m-10) REVERT: C 38 VAL cc_start: 0.8238 (t) cc_final: 0.7869 (t) REVERT: C 39 TYR cc_start: 0.8822 (m-80) cc_final: 0.8600 (m-80) REVERT: C 114 GLN cc_start: 0.8755 (tp40) cc_final: 0.7552 (tm-30) REVERT: C 199 SER cc_start: 0.9443 (p) cc_final: 0.9096 (t) REVERT: C 369 LEU cc_start: 0.8533 (tp) cc_final: 0.8293 (mp) REVERT: D 577 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7878 (tm-30) REVERT: D 601 LYS cc_start: 0.9143 (ptpt) cc_final: 0.8910 (ptpp) REVERT: D 610 TRP cc_start: 0.8012 (t-100) cc_final: 0.7811 (t-100) REVERT: E 103 GLN cc_start: 0.8296 (tt0) cc_final: 0.8024 (tm-30) REVERT: E 150 MET cc_start: 0.8018 (mmm) cc_final: 0.7688 (mmt) REVERT: E 381 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7082 (tt0) REVERT: E 500 ARG cc_start: 0.5831 (mtt180) cc_final: 0.5028 (pmt170) REVERT: F 607 ASN cc_start: 0.9025 (p0) cc_final: 0.8401 (p0) REVERT: F 634 GLU cc_start: 0.8675 (mt-10) cc_final: 0.7836 (mm-30) REVERT: F 642 ILE cc_start: 0.9562 (mt) cc_final: 0.9335 (mm) REVERT: F 648 GLU cc_start: 0.8468 (tp30) cc_final: 0.8246 (tp30) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1177 time to fit residues: 48.5292 Evaluate side-chains 222 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 85 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 0.0170 chunk 128 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.9618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN E 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.087294 restraints weight = 35835.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089718 restraints weight = 21542.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091392 restraints weight = 15285.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092531 restraints weight = 12050.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093223 restraints weight = 10196.261| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 0.083 16194 Z= 0.146 Angle : 0.705 16.471 22182 Z= 0.335 Chirality : 0.047 0.402 2773 Planarity : 0.004 0.053 2679 Dihedral : 4.679 22.616 2025 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 0.07 % Allowed : 1.24 % Favored : 98.69 % 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 are not related in a simple way. whole: 0.51 (0.20), residues: 1678 helix: 1.84 (0.26), residues: 421 sheet: 0.60 (0.24), residues: 436 loop : -0.58 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 585 TYR 0.016 0.001 TYR E 173 PHE 0.014 0.002 PHE C 93 TRP 0.053 0.002 TRP C 69 HIS 0.007 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (16072) covalent geometry : angle 0.65044 / 0.32 (21852) SS BOND : bond 0.00397 / 0.28 ( 36) SS BOND : angle 1.53957 / 1.21 ( 72) hydrogen bonds : bond 0.04438 / 2.99 ( 650) hydrogen bonds : angle 5.28011 / 3.70 ( 1797) link_ALPHA1-2 : bond 0.00756 / 0.39 ( 2) link_ALPHA1-2 : angle 1.72330 / 1.41 ( 6) link_ALPHA1-3 : bond 0.01259 / 0.61 ( 4) link_ALPHA1-3 : angle 2.02666 / 1.47 ( 12) link_ALPHA1-6 : bond 0.00851 / 0.43 ( 4) link_ALPHA1-6 : angle 1.50649 / 1.13 ( 12) link_BETA1-4 : bond 0.00467 / 0.30 ( 11) link_BETA1-4 : angle 1.43084 / 0.88 ( 33) link_NAG-ASN : bond 0.00466 / 0.27 ( 65) link_NAG-ASN : angle 2.73740 / 1.87 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 THR cc_start: 0.9514 (m) cc_final: 0.9136 (p) REVERT: A 217 TYR cc_start: 0.8324 (m-10) cc_final: 0.7602 (m-10) REVERT: A 256 SER cc_start: 0.9386 (p) cc_final: 0.9100 (m) REVERT: A 315 GLN cc_start: 0.8628 (mp10) cc_final: 0.8267 (mp10) REVERT: B 535 MET cc_start: 0.7601 (mpp) cc_final: 0.7309 (mmt) REVERT: B 560 GLU cc_start: 0.7615 (mp0) cc_final: 0.7328 (mm-30) REVERT: B 596 TRP cc_start: 0.8598 (m-10) cc_final: 0.8297 (m-10) REVERT: B 599 SER cc_start: 0.8885 (p) cc_final: 0.8392 (t) REVERT: B 628 TRP cc_start: 0.7778 (m100) cc_final: 0.7540 (m100) REVERT: B 641 ILE cc_start: 0.8106 (mp) cc_final: 0.7635 (tp) REVERT: B 643 TYR cc_start: 0.9064 (m-10) cc_final: 0.8794 (m-10) REVERT: B 647 GLU cc_start: 0.8222 (pt0) cc_final: 0.7620 (pt0) REVERT: C 38 VAL cc_start: 0.8113 (t) cc_final: 0.7889 (t) REVERT: C 114 GLN cc_start: 0.8723 (tp40) cc_final: 0.7528 (tm-30) REVERT: C 150 MET cc_start: 0.8772 (ppp) cc_final: 0.8101 (ppp) REVERT: C 199 SER cc_start: 0.9491 (p) cc_final: 0.9121 (t) REVERT: D 571 TRP cc_start: 0.6677 (t60) cc_final: 0.6413 (t60) REVERT: D 577 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7793 (tm-30) REVERT: D 586 TYR cc_start: 0.9250 (t80) cc_final: 0.8940 (t80) REVERT: D 588 ARG cc_start: 0.8855 (tmm-80) cc_final: 0.8649 (ttp80) REVERT: D 601 LYS cc_start: 0.9171 (ptpt) cc_final: 0.8832 (ptpp) REVERT: E 103 GLN cc_start: 0.8041 (tt0) cc_final: 0.7753 (tm-30) REVERT: E 150 MET cc_start: 0.8008 (mmm) cc_final: 0.7718 (mmt) REVERT: E 381 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7012 (tt0) REVERT: E 500 ARG cc_start: 0.6118 (mtt180) cc_final: 0.5229 (pmt170) REVERT: F 607 ASN cc_start: 0.9015 (p0) cc_final: 0.8339 (p0) REVERT: F 626 MET cc_start: 0.7528 (ttm) cc_final: 0.7293 (ttm) REVERT: F 628 TRP cc_start: 0.8421 (m100) cc_final: 0.8130 (m100) REVERT: F 629 LEU cc_start: 0.8096 (mt) cc_final: 0.7352 (mt) REVERT: F 633 LYS cc_start: 0.8080 (mppt) cc_final: 0.7808 (mmtm) REVERT: F 634 GLU cc_start: 0.8643 (mt-10) cc_final: 0.7806 (mm-30) REVERT: F 642 ILE cc_start: 0.9539 (mt) cc_final: 0.9290 (mm) outliers start: 1 outliers final: 1 residues processed: 278 average time/residue: 0.1192 time to fit residues: 49.4785 Evaluate side-chains 225 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 114 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS E 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.085929 restraints weight = 36288.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088290 restraints weight = 21871.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.089940 restraints weight = 15623.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.091068 restraints weight = 12344.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091737 restraints weight = 10459.630| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16194 Z= 0.184 Angle : 0.717 16.370 22182 Z= 0.345 Chirality : 0.047 0.382 2773 Planarity : 0.004 0.050 2679 Dihedral : 4.714 20.867 2025 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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 are not related in a simple way. whole: 0.43 (0.20), residues: 1678 helix: 1.79 (0.26), residues: 422 sheet: 0.55 (0.25), residues: 432 loop : -0.64 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 585 TYR 0.019 0.002 TYR A 217 PHE 0.015 0.002 PHE A 361 TRP 0.044 0.002 TRP C 69 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (16072) covalent geometry : angle 0.66752 / 0.33 (21852) SS BOND : bond 0.00417 / 0.29 ( 36) SS BOND : angle 1.55830 / 1.15 ( 72) hydrogen bonds : bond 0.04541 / 3.06 ( 650) hydrogen bonds : angle 5.25238 / 3.68 ( 1797) link_ALPHA1-2 : bond 0.00635 / 0.32 ( 2) link_ALPHA1-2 : angle 1.79502 / 1.48 ( 6) link_ALPHA1-3 : bond 0.01123 / 0.54 ( 4) link_ALPHA1-3 : angle 2.08380 / 1.45 ( 12) link_ALPHA1-6 : bond 0.00928 / 0.46 ( 4) link_ALPHA1-6 : angle 1.59704 / 1.18 ( 12) link_BETA1-4 : bond 0.00388 / 0.26 ( 11) link_BETA1-4 : angle 1.47364 / 0.90 ( 33) link_NAG-ASN : bond 0.00414 / 0.25 ( 65) link_NAG-ASN : angle 2.58453 / 1.77 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9090 (tpp) cc_final: 0.8494 (tpt) REVERT: A 256 SER cc_start: 0.9384 (p) cc_final: 0.9084 (m) REVERT: A 275 GLU cc_start: 0.8059 (mp0) cc_final: 0.7829 (mp0) REVERT: A 315 GLN cc_start: 0.8698 (mp10) cc_final: 0.8401 (mp10) REVERT: B 535 MET cc_start: 0.7629 (mpp) cc_final: 0.7410 (mmt) REVERT: B 560 GLU cc_start: 0.7625 (mp0) cc_final: 0.7296 (mm-30) REVERT: B 599 SER cc_start: 0.8907 (p) cc_final: 0.8429 (t) REVERT: B 641 ILE cc_start: 0.8131 (mp) cc_final: 0.7651 (tp) REVERT: B 643 TYR cc_start: 0.9093 (m-10) cc_final: 0.8868 (m-10) REVERT: C 38 VAL cc_start: 0.8169 (t) cc_final: 0.7862 (t) REVERT: C 39 TYR cc_start: 0.8795 (m-80) cc_final: 0.8581 (m-80) REVERT: C 114 GLN cc_start: 0.8775 (tp40) cc_final: 0.7572 (tm-30) REVERT: C 150 MET cc_start: 0.8812 (ppp) cc_final: 0.8127 (ppp) REVERT: C 161 MET cc_start: 0.8768 (tpp) cc_final: 0.8482 (tpt) REVERT: C 199 SER cc_start: 0.9441 (p) cc_final: 0.9113 (t) REVERT: C 295 ASN cc_start: 0.8493 (m-40) cc_final: 0.8083 (m-40) REVERT: D 571 TRP cc_start: 0.6909 (t60) cc_final: 0.6580 (t60) REVERT: D 577 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 586 TYR cc_start: 0.9386 (t80) cc_final: 0.8954 (t80) REVERT: D 601 LYS cc_start: 0.9234 (ptpt) cc_final: 0.8810 (ptpp) REVERT: E 95 MET cc_start: 0.8955 (ppp) cc_final: 0.8658 (ppp) REVERT: E 103 GLN cc_start: 0.8228 (tt0) cc_final: 0.8003 (tm-30) REVERT: E 150 MET cc_start: 0.8002 (mmm) cc_final: 0.7755 (mmt) REVERT: E 161 MET cc_start: 0.8833 (tpp) cc_final: 0.8338 (ttm) REVERT: E 381 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7042 (tt0) REVERT: E 500 ARG cc_start: 0.5965 (mtt180) cc_final: 0.5276 (pmt170) REVERT: F 536 THR cc_start: 0.8474 (p) cc_final: 0.8260 (p) REVERT: F 607 ASN cc_start: 0.9031 (p0) cc_final: 0.8355 (p0) REVERT: F 628 TRP cc_start: 0.8444 (m100) cc_final: 0.8242 (m100) REVERT: F 634 GLU cc_start: 0.8624 (mt-10) cc_final: 0.7759 (mm-30) REVERT: F 642 ILE cc_start: 0.9574 (mt) cc_final: 0.9362 (mm) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1255 time to fit residues: 51.2126 Evaluate side-chains 216 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 65 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.087112 restraints weight = 35984.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089457 restraints weight = 21750.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.091104 restraints weight = 15544.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092198 restraints weight = 12264.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092986 restraints weight = 10418.749| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16194 Z= 0.158 Angle : 0.703 16.252 22182 Z= 0.341 Chirality : 0.047 0.404 2773 Planarity : 0.004 0.052 2679 Dihedral : 4.684 25.211 2025 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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 are not related in a simple way. whole: 0.33 (0.20), residues: 1678 helix: 1.74 (0.26), residues: 421 sheet: 0.49 (0.25), residues: 434 loop : -0.73 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 585 TYR 0.019 0.002 TYR A 217 PHE 0.016 0.002 PHE C 93 TRP 0.075 0.002 TRP D 610 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (16072) covalent geometry : angle 0.65618 / 0.33 (21852) SS BOND : bond 0.00406 / 0.28 ( 36) SS BOND : angle 1.48923 / 1.08 ( 72) hydrogen bonds : bond 0.04459 / 3.00 ( 650) hydrogen bonds : angle 5.22421 / 3.67 ( 1797) link_ALPHA1-2 : bond 0.00686 / 0.35 ( 2) link_ALPHA1-2 : angle 1.70263 / 1.39 ( 6) link_ALPHA1-3 : bond 0.01091 / 0.53 ( 4) link_ALPHA1-3 : angle 2.00775 / 1.37 ( 12) link_ALPHA1-6 : bond 0.00920 / 0.46 ( 4) link_ALPHA1-6 : angle 1.53562 / 1.11 ( 12) link_BETA1-4 : bond 0.00401 / 0.26 ( 11) link_BETA1-4 : angle 1.39253 / 0.86 ( 33) link_NAG-ASN : bond 0.00397 / 0.23 ( 65) link_NAG-ASN : angle 2.51293 / 1.72 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9073 (tpp) cc_final: 0.8814 (tpp) REVERT: A 202 THR cc_start: 0.9510 (m) cc_final: 0.9142 (p) REVERT: A 256 SER cc_start: 0.9389 (p) cc_final: 0.9116 (m) REVERT: A 315 GLN cc_start: 0.8703 (mp10) cc_final: 0.8351 (mp10) REVERT: A 462 ASN cc_start: 0.7909 (t0) cc_final: 0.7670 (t0) REVERT: B 535 MET cc_start: 0.7637 (mpp) cc_final: 0.7351 (mmt) REVERT: B 560 GLU cc_start: 0.7557 (mp0) cc_final: 0.7185 (mm-30) REVERT: B 641 ILE cc_start: 0.8120 (mp) cc_final: 0.7459 (tp) REVERT: C 38 VAL cc_start: 0.8036 (t) cc_final: 0.7646 (t) REVERT: C 39 TYR cc_start: 0.8752 (m-80) cc_final: 0.8523 (m-80) REVERT: C 114 GLN cc_start: 0.8704 (tp40) cc_final: 0.7564 (tm-30) REVERT: C 150 MET cc_start: 0.8774 (ppp) cc_final: 0.8189 (ppp) REVERT: C 161 MET cc_start: 0.8774 (tpp) cc_final: 0.8544 (tpt) REVERT: C 199 SER cc_start: 0.9406 (p) cc_final: 0.9119 (t) REVERT: C 295 ASN cc_start: 0.8390 (m-40) cc_final: 0.7988 (m-40) REVERT: C 369 LEU cc_start: 0.8521 (tp) cc_final: 0.8205 (mp) REVERT: D 577 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7866 (tm-30) REVERT: D 586 TYR cc_start: 0.9358 (t80) cc_final: 0.9065 (t80) REVERT: D 610 TRP cc_start: 0.7424 (t60) cc_final: 0.7075 (t60) REVERT: D 614 TRP cc_start: 0.8422 (m-10) cc_final: 0.8210 (m-10) REVERT: E 95 MET cc_start: 0.8899 (ppp) cc_final: 0.8516 (ppp) REVERT: E 103 GLN cc_start: 0.8181 (tt0) cc_final: 0.7884 (tm-30) REVERT: E 104 MET cc_start: 0.8695 (ttt) cc_final: 0.8494 (tpp) REVERT: E 150 MET cc_start: 0.7991 (mmm) cc_final: 0.7784 (mmt) REVERT: E 161 MET cc_start: 0.8797 (tpp) cc_final: 0.8352 (ttm) REVERT: E 381 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7371 (tt0) REVERT: E 500 ARG cc_start: 0.5985 (mtt180) cc_final: 0.5275 (pmt170) REVERT: F 607 ASN cc_start: 0.9026 (p0) cc_final: 0.8323 (p0) REVERT: F 628 TRP cc_start: 0.8457 (m100) cc_final: 0.8252 (m100) REVERT: F 634 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7689 (mm-30) REVERT: F 642 ILE cc_start: 0.9576 (mt) cc_final: 0.9364 (mm) REVERT: F 654 GLU cc_start: 0.9083 (tp30) cc_final: 0.8820 (tp30) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1327 time to fit residues: 54.4513 Evaluate side-chains 215 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 85 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 52 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 170 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.088139 restraints weight = 35563.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.090564 restraints weight = 21354.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092208 restraints weight = 15104.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093252 restraints weight = 11908.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094079 restraints weight = 10151.686| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16194 Z= 0.137 Angle : 0.679 16.254 22182 Z= 0.331 Chirality : 0.046 0.391 2773 Planarity : 0.004 0.051 2679 Dihedral : 4.570 23.061 2025 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 are not related in a simple way. whole: 0.38 (0.20), residues: 1678 helix: 1.82 (0.26), residues: 420 sheet: 0.49 (0.25), residues: 438 loop : -0.70 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 585 TYR 0.021 0.001 TYR A 217 PHE 0.013 0.002 PHE C 210 TRP 0.055 0.002 TRP D 610 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16072) covalent geometry : angle 0.63597 / 0.32 (21852) SS BOND : bond 0.00374 / 0.26 ( 36) SS BOND : angle 1.43257 / 1.04 ( 72) hydrogen bonds : bond 0.04253 / 2.87 ( 650) hydrogen bonds : angle 5.10325 / 3.59 ( 1797) link_ALPHA1-2 : bond 0.00731 / 0.37 ( 2) link_ALPHA1-2 : angle 1.66449 / 1.34 ( 6) link_ALPHA1-3 : bond 0.01070 / 0.52 ( 4) link_ALPHA1-3 : angle 1.93089 / 1.30 ( 12) link_ALPHA1-6 : bond 0.00959 / 0.48 ( 4) link_ALPHA1-6 : angle 1.49656 / 1.06 ( 12) link_BETA1-4 : bond 0.00433 / 0.28 ( 11) link_BETA1-4 : angle 1.33587 / 0.83 ( 33) link_NAG-ASN : bond 0.00389 / 0.23 ( 65) link_NAG-ASN : angle 2.37046 / 1.62 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9036 (tpp) cc_final: 0.8809 (tpt) REVERT: A 153 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8230 (tp30) REVERT: A 178 ARG cc_start: 0.8108 (tpt90) cc_final: 0.7841 (tpt90) REVERT: A 202 THR cc_start: 0.9492 (m) cc_final: 0.9036 (p) REVERT: A 256 SER cc_start: 0.9352 (p) cc_final: 0.9071 (m) REVERT: A 315 GLN cc_start: 0.8504 (mp10) cc_final: 0.8234 (mp10) REVERT: B 535 MET cc_start: 0.7662 (mpp) cc_final: 0.7387 (mmt) REVERT: B 560 GLU cc_start: 0.7737 (mp0) cc_final: 0.7316 (mm-30) REVERT: B 641 ILE cc_start: 0.8113 (mp) cc_final: 0.7433 (tp) REVERT: C 38 VAL cc_start: 0.8016 (t) cc_final: 0.7687 (t) REVERT: C 112 TRP cc_start: 0.8525 (m100) cc_final: 0.8239 (t-100) REVERT: C 114 GLN cc_start: 0.8691 (tp40) cc_final: 0.7580 (tm-30) REVERT: C 150 MET cc_start: 0.8735 (ppp) cc_final: 0.8207 (ppp) REVERT: C 199 SER cc_start: 0.9389 (p) cc_final: 0.9093 (t) REVERT: C 295 ASN cc_start: 0.8307 (m-40) cc_final: 0.7960 (m-40) REVERT: D 577 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7849 (tm-30) REVERT: D 586 TYR cc_start: 0.9336 (t80) cc_final: 0.9047 (t80) REVERT: D 588 ARG cc_start: 0.8927 (ttp80) cc_final: 0.8718 (tmm-80) REVERT: D 610 TRP cc_start: 0.7382 (t60) cc_final: 0.7084 (t60) REVERT: D 623 TRP cc_start: 0.8370 (m100) cc_final: 0.7508 (m-10) REVERT: E 95 MET cc_start: 0.8871 (ppp) cc_final: 0.8503 (ppp) REVERT: E 103 GLN cc_start: 0.8145 (tt0) cc_final: 0.7843 (tm-30) REVERT: E 161 MET cc_start: 0.8763 (tpp) cc_final: 0.8327 (ttm) REVERT: E 381 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7274 (tt0) REVERT: E 500 ARG cc_start: 0.5983 (mtt180) cc_final: 0.5304 (pmt170) REVERT: F 536 THR cc_start: 0.8819 (p) cc_final: 0.8616 (p) REVERT: F 607 ASN cc_start: 0.9022 (p0) cc_final: 0.8337 (p0) REVERT: F 634 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7550 (mm-30) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1215 time to fit residues: 50.4562 Evaluate side-chains 231 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 146 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 120 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 169 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089689 restraints weight = 35707.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092139 restraints weight = 21360.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093807 restraints weight = 15055.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094940 restraints weight = 11826.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095699 restraints weight = 10003.295| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16194 Z= 0.126 Angle : 0.668 16.131 22182 Z= 0.324 Chirality : 0.046 0.384 2773 Planarity : 0.004 0.051 2679 Dihedral : 4.500 28.608 2025 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 are not related in a simple way. whole: 0.42 (0.20), residues: 1678 helix: 1.83 (0.26), residues: 424 sheet: 0.61 (0.25), residues: 432 loop : -0.72 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 585 TYR 0.030 0.001 TYR D 643 PHE 0.016 0.001 PHE C 210 TRP 0.068 0.002 TRP D 614 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (16072) covalent geometry : angle 0.62564 / 0.31 (21852) SS BOND : bond 0.00352 / 0.25 ( 36) SS BOND : angle 1.34413 / 0.99 ( 72) hydrogen bonds : bond 0.04057 / 2.72 ( 650) hydrogen bonds : angle 5.05432 / 3.55 ( 1797) link_ALPHA1-2 : bond 0.00772 / 0.39 ( 2) link_ALPHA1-2 : angle 1.63915 / 1.30 ( 6) link_ALPHA1-3 : bond 0.01031 / 0.50 ( 4) link_ALPHA1-3 : angle 1.88264 / 1.24 ( 12) link_ALPHA1-6 : bond 0.00963 / 0.48 ( 4) link_ALPHA1-6 : angle 1.45717 / 1.01 ( 12) link_BETA1-4 : bond 0.00462 / 0.29 ( 11) link_BETA1-4 : angle 1.29290 / 0.82 ( 33) link_NAG-ASN : bond 0.00387 / 0.24 ( 65) link_NAG-ASN : angle 2.35642 / 1.62 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.54 seconds wall clock time: 41 minutes 33.59 seconds (2493.59 seconds total)