Starting phenix.real_space_refine on Fri Sep 27 14:16:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/09_2024/7t73_25732.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/09_2024/7t73_25732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/09_2024/7t73_25732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/09_2024/7t73_25732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/09_2024/7t73_25732.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t73_25732/09_2024/7t73_25732.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.120 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 107 5.16 5 C 9994 2.51 5 N 2660 2.21 5 O 3249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16010 Number of models: 1 Model: "" Number of chains: 28 Chain: "H" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1046 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 801 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3458 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 23, 'TRANS': 417} Chain breaks: 2 Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3392 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 2 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3458 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 23, 'TRANS': 417} Chain breaks: 2 Chain: "D" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.76, per 1000 atoms: 0.61 Number of scatterers: 16010 At special positions: 0 Unit cell: (129.95, 128.8, 156.4, 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 107 16.00 O 3249 8.00 N 2660 7.00 C 9994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.19 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 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=2.17 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=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.18 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=2.23 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.14 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 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=2.09 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 D 598 " - pdb=" SG CYS D 604 " distance=2.02 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 ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 7 " " MAN V 4 " - " MAN V 5 " ALPHA1-6 " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 332 " " NAG A 608 " - " ASN A 355 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 197 " " NAG A 611 " - " ASN A 339 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 618 " " NAG C 601 " - " ASN C 197 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 332 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 276 " " NAG C 608 " - " ASN C 392 " " NAG C 609 " - " ASN C 88 " " NAG C 610 " - " ASN C 339 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E1001 " - " ASN E 197 " " NAG E1002 " - " ASN E 301 " " NAG E1003 " - " ASN E 448 " " NAG E1004 " - " ASN E 276 " " NAG E1005 " - " ASN E 392 " " NAG E1006 " - " ASN E 88 " " NAG E1007 " - " ASN E 339 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 160 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 386 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN E 156 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 332 " " NAG U 1 " - " ASN E 386 " " NAG V 1 " - " ASN E 160 " Time building additional restraints: 5.35 Conformation dependent library (CDL) restraints added in 2.0 seconds 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 30 sheets defined 23.3% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.187A 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 335 through 350 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.273A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.516A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.597A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 660 removed outlier: 4.509A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.906A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 460 through 464 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.898A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.147A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 341 through 353 removed outlier: 3.824A pdb=" N VAL E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.712A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 537 No H-bonds generated for 'chain 'D' and resid 535 through 537' Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.120A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.762A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 639 through 650 Processing helix chain 'D' and resid 651 through 653 No H-bonds generated for 'chain 'D' and resid 651 through 653' Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.276A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.977A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 Processing helix chain 'F' and resid 620 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 650 removed outlier: 4.295A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 660 removed outlier: 4.219A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.822A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 103 Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.695A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.469A pdb=" N VAL A 242 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 87 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.665A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.869A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 132 removed outlier: 4.231A pdb=" N THR A 132 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AB2, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.523A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 393 through 395 current: chain 'A' and resid 466 through 470 Processing sheet with id=AB3, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB4, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB5, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.305A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.752A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU C 86 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.601A pdb=" N THR C 132 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 202 removed outlier: 6.359A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 283 through 298 removed outlier: 6.923A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 467 through 470 Processing sheet with id=AC3, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.545A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC6, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.520A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC8, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.532A pdb=" N GLN E 130 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AD1, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 3.702A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AD3, first strand: chain 'E' and resid 423 through 424 401 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.32: 3006 1.32 - 1.49: 6620 1.49 - 1.66: 6556 1.66 - 1.83: 107 1.83 - 2.00: 34 Bond restraints: 16323 Sorted by residual: bond pdb=" CA SER E 174 " pdb=" CB SER E 174 " ideal model delta sigma weight residual 1.533 1.377 0.156 1.60e-02 3.91e+03 9.47e+01 bond pdb=" CA SER E 158 " pdb=" CB SER E 158 " ideal model delta sigma weight residual 1.532 1.388 0.144 1.58e-02 4.01e+03 8.31e+01 bond pdb=" C LEU E 175 " pdb=" O LEU E 175 " ideal model delta sigma weight residual 1.236 1.146 0.090 1.21e-02 6.83e+03 5.53e+01 bond pdb=" CB ILE L 106 " pdb=" CG1 ILE L 106 " ideal model delta sigma weight residual 1.530 1.674 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C SER E 158 " pdb=" O SER E 158 " ideal model delta sigma weight residual 1.235 1.158 0.078 1.12e-02 7.97e+03 4.80e+01 ... (remaining 16318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.61: 22106 7.61 - 15.22: 69 15.22 - 22.83: 1 22.83 - 30.44: 0 30.44 - 38.05: 4 Bond angle restraints: 22180 Sorted by residual: angle pdb=" C ASN E 156 " pdb=" CA ASN E 156 " pdb=" CB ASN E 156 " ideal model delta sigma weight residual 110.22 88.52 21.70 1.67e+00 3.59e-01 1.69e+02 angle pdb=" C2 NAG U 1 " pdb=" N2 NAG U 1 " pdb=" C7 NAG U 1 " ideal model delta sigma weight residual 124.56 162.61 -38.05 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C2 NAG A 609 " pdb=" N2 NAG A 609 " pdb=" C7 NAG A 609 " ideal model delta sigma weight residual 124.56 161.28 -36.72 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 160.09 -35.53 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG A 603 " pdb=" N2 NAG A 603 " pdb=" C7 NAG A 603 " ideal model delta sigma weight residual 124.56 158.89 -34.33 3.00e+00 1.11e-01 1.31e+02 ... (remaining 22175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 10343 21.90 - 43.80: 288 43.80 - 65.70: 93 65.70 - 87.60: 48 87.60 - 109.50: 28 Dihedral angle restraints: 10800 sinusoidal: 5313 harmonic: 5487 Sorted by residual: dihedral pdb=" C ASN E 156 " pdb=" N ASN E 156 " pdb=" CA ASN E 156 " pdb=" CB ASN E 156 " ideal model delta harmonic sigma weight residual -122.60 -93.57 -29.03 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" CB CYS D 598 " pdb=" SG CYS D 598 " pdb=" SG CYS D 604 " pdb=" CB CYS D 604 " ideal model delta sinusoidal sigma weight residual -86.00 -176.12 90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 169.05 -76.05 1 1.00e+01 1.00e-02 7.29e+01 ... (remaining 10797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 2578 0.307 - 0.614: 140 0.614 - 0.922: 1 0.922 - 1.229: 0 1.229 - 1.536: 1 Chirality restraints: 2720 Sorted by residual: chirality pdb=" C1 MAN V 4 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 4.99e+02 chirality pdb=" C1 MAN V 6 " pdb=" O6 MAN V 4 " pdb=" C2 MAN V 6 " pdb=" O5 MAN V 6 " both_signs ideal model delta sigma weight residual False 2.40 2.08 0.32 2.00e-02 2.50e+03 2.60e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 ... (remaining 2717 not shown) Planarity restraints: 2786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.372 2.00e-02 2.50e+03 3.17e-01 1.26e+03 pdb=" C7 NAG N 1 " -0.096 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.135 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.561 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 703 " -0.345 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG D 703 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG D 703 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG D 703 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG D 703 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 701 " 0.339 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B 701 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG B 701 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG B 701 " -0.496 2.00e-02 2.50e+03 pdb=" O7 NAG B 701 " 0.056 2.00e-02 2.50e+03 ... (remaining 2783 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 1 2.20 - 2.87: 5544 2.87 - 3.55: 20487 3.55 - 4.22: 38529 4.22 - 4.90: 59536 Nonbonded interactions: 124097 Sorted by model distance: nonbonded pdb=" OG SER F 613 " pdb=" C1 NAG F 701 " model vdw 1.521 3.470 nonbonded pdb=" O5 NAG B 702 " pdb=" O6 NAG B 702 " model vdw 2.217 2.432 nonbonded pdb=" OG SER F 613 " pdb=" O5 NAG F 701 " model vdw 2.244 3.040 nonbonded pdb=" O5 NAG N 1 " pdb=" O6 NAG N 1 " model vdw 2.262 2.432 nonbonded pdb=" O ASN E 136 " pdb=" CB ASN E 136 " model vdw 2.268 2.752 ... (remaining 124092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 57 or resid 74 through 501 or resid 601 through \ 607)) selection = (chain 'C' and (resid 32 through 501 or resid 601 through 607)) selection = (chain 'E' and (resid 32 through 57 or resid 74 through 501 or resid 1001 throug \ h 1007)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'R' } 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.080 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.021 0.190 16323 Z= 1.343 Angle : 1.921 38.047 22180 Z= 1.219 Chirality : 0.145 1.536 2720 Planarity : 0.018 0.317 2735 Dihedral : 13.611 109.497 7160 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.80 % Allowed : 3.48 % Favored : 95.72 % Rotamer: Outliers : 1.56 % Allowed : 1.38 % Favored : 97.07 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 1867 helix: -1.13 (0.24), residues: 355 sheet: -0.07 (0.23), residues: 477 loop : -0.16 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.009 TRP E 479 HIS 0.011 0.002 HIS D 585 PHE 0.062 0.006 PHE E 159 TYR 0.048 0.007 TYR C 191 ARG 0.014 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 503 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 THR cc_start: 0.3110 (t) cc_final: 0.2275 (m) REVERT: L 48 ILE cc_start: 0.7032 (mt) cc_final: 0.6814 (tt) REVERT: A 35 TRP cc_start: 0.8285 (m100) cc_final: 0.7597 (m-10) REVERT: A 104 MET cc_start: 0.9451 (ttt) cc_final: 0.9239 (ttp) REVERT: A 287 GLN cc_start: 0.7552 (tt0) cc_final: 0.7110 (mm110) REVERT: A 426 MET cc_start: 0.7700 (ttt) cc_final: 0.7230 (tpt) REVERT: B 626 MET cc_start: 0.7680 (mtp) cc_final: 0.7475 (mtt) REVERT: B 632 ASP cc_start: 0.8720 (t70) cc_final: 0.8425 (t70) REVERT: C 82 GLN cc_start: 0.7248 (mt0) cc_final: 0.7044 (tt0) REVERT: C 97 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7570 (tptp) REVERT: C 129 LEU cc_start: 0.9191 (mt) cc_final: 0.8966 (mp) REVERT: C 156 ASN cc_start: 0.9315 (t0) cc_final: 0.8820 (t0) REVERT: C 168 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7289 (mtmm) REVERT: C 217 TYR cc_start: 0.8640 (m-80) cc_final: 0.8223 (m-80) REVERT: C 492 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8317 (mt-10) REVERT: C 498 PRO cc_start: 0.9499 (OUTLIER) cc_final: 0.8849 (Cg_exo) REVERT: E 194 ILE cc_start: 0.8929 (tp) cc_final: 0.8430 (tt) REVERT: E 264 SER cc_start: 0.8447 (t) cc_final: 0.7786 (m) REVERT: E 282 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8947 (mmmt) REVERT: D 522 PHE cc_start: 0.9223 (t80) cc_final: 0.8954 (t80) REVERT: D 536 THR cc_start: 0.7947 (p) cc_final: 0.7438 (t) REVERT: D 610 TRP cc_start: 0.8843 (t-100) cc_final: 0.8381 (t-100) REVERT: D 616 ASN cc_start: 0.7344 (p0) cc_final: 0.7143 (p0) REVERT: D 623 TRP cc_start: 0.8951 (m100) cc_final: 0.8032 (m100) REVERT: D 643 TYR cc_start: 0.8532 (m-10) cc_final: 0.8275 (m-80) REVERT: F 543 ASN cc_start: 0.8597 (m-40) cc_final: 0.8221 (m-40) REVERT: F 601 LYS cc_start: 0.8900 (mttt) cc_final: 0.8666 (mmtp) outliers start: 26 outliers final: 8 residues processed: 520 average time/residue: 0.2915 time to fit residues: 219.6094 Evaluate side-chains 279 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 270 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 498 PRO Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain F residue 615 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 103 GLN A 170 GLN A 203 GLN B 591 GLN C 85 HIS C 234 ASN C 300 ASN C 363 GLN E 136 ASN E 425 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16323 Z= 0.281 Angle : 0.791 11.130 22180 Z= 0.396 Chirality : 0.051 0.278 2720 Planarity : 0.004 0.033 2735 Dihedral : 10.951 86.180 3663 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 2.93 % Allowed : 10.77 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 1867 helix: -0.04 (0.28), residues: 339 sheet: 0.07 (0.23), residues: 478 loop : -0.56 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 610 HIS 0.006 0.001 HIS C 85 PHE 0.029 0.003 PHE E 233 TYR 0.022 0.002 TYR C 217 ARG 0.006 0.001 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 313 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7130 (tp) REVERT: A 35 TRP cc_start: 0.7975 (m100) cc_final: 0.7532 (m-10) REVERT: A 103 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6839 (tm130) REVERT: A 106 GLU cc_start: 0.8768 (tt0) cc_final: 0.8179 (tp30) REVERT: A 120 VAL cc_start: 0.9200 (m) cc_final: 0.8976 (p) REVERT: A 168 LYS cc_start: 0.8557 (mmtt) cc_final: 0.7922 (ttpt) REVERT: A 287 GLN cc_start: 0.7569 (tt0) cc_final: 0.7193 (mm-40) REVERT: A 486 TYR cc_start: 0.8813 (m-80) cc_final: 0.8055 (m-80) REVERT: B 535 MET cc_start: 0.8340 (mmm) cc_final: 0.8003 (mmm) REVERT: B 628 TRP cc_start: 0.9233 (m100) cc_final: 0.8317 (m100) REVERT: B 640 GLN cc_start: 0.8668 (mp10) cc_final: 0.8327 (mp10) REVERT: B 648 GLU cc_start: 0.7751 (tp30) cc_final: 0.7297 (tp30) REVERT: C 97 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7948 (tptp) REVERT: C 112 TRP cc_start: 0.8399 (t-100) cc_final: 0.8119 (t-100) REVERT: C 168 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7355 (mtmm) REVERT: C 210 PHE cc_start: 0.8296 (m-80) cc_final: 0.7737 (m-80) REVERT: C 278 THR cc_start: 0.9075 (p) cc_final: 0.8658 (t) REVERT: C 492 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8312 (mt-10) REVERT: E 194 ILE cc_start: 0.8703 (tp) cc_final: 0.8376 (tt) REVERT: E 256 SER cc_start: 0.8765 (p) cc_final: 0.8498 (m) REVERT: E 282 LYS cc_start: 0.9263 (mmtt) cc_final: 0.8971 (mmmt) REVERT: E 426 MET cc_start: 0.8095 (tpt) cc_final: 0.7676 (tpt) REVERT: D 538 THR cc_start: 0.9116 (p) cc_final: 0.8834 (p) REVERT: D 592 LEU cc_start: 0.8472 (tp) cc_final: 0.7928 (mt) REVERT: D 610 TRP cc_start: 0.8996 (t-100) cc_final: 0.8509 (t-100) REVERT: D 639 THR cc_start: 0.8728 (p) cc_final: 0.8244 (m) REVERT: D 653 GLN cc_start: 0.7861 (mp10) cc_final: 0.7607 (mp10) REVERT: F 530 MET cc_start: 0.8393 (mtm) cc_final: 0.8043 (mtp) REVERT: F 543 ASN cc_start: 0.8426 (m-40) cc_final: 0.7864 (t0) REVERT: F 601 LYS cc_start: 0.8871 (mttt) cc_final: 0.8655 (mmtp) REVERT: F 610 TRP cc_start: 0.9178 (t-100) cc_final: 0.8719 (t-100) outliers start: 49 outliers final: 29 residues processed: 348 average time/residue: 0.2860 time to fit residues: 150.0131 Evaluate side-chains 277 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 246 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 630 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 170 optimal weight: 0.3980 chunk 183 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN L 89 GLN A 103 GLN B 543 ASN B 625 ASN B 653 GLN E 203 GLN E 258 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16323 Z= 0.239 Angle : 0.689 10.841 22180 Z= 0.347 Chirality : 0.048 0.270 2720 Planarity : 0.004 0.040 2735 Dihedral : 8.933 68.826 3654 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.05 % Favored : 96.79 % Rotamer: Outliers : 3.35 % Allowed : 12.27 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1867 helix: -0.17 (0.27), residues: 363 sheet: 0.10 (0.24), residues: 465 loop : -0.77 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 103 HIS 0.005 0.001 HIS A 72 PHE 0.019 0.002 PHE E 93 TYR 0.019 0.002 TYR L 86 ARG 0.005 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 272 time to evaluate : 1.782 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: H 78 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6590 (tp) REVERT: H 82 MET cc_start: 0.6001 (mmt) cc_final: 0.3866 (tpp) REVERT: H 90 TYR cc_start: 0.3443 (m-80) cc_final: 0.3232 (m-10) REVERT: H 111 VAL cc_start: 0.5233 (t) cc_final: 0.4975 (t) REVERT: L 38 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7494 (tp40) REVERT: A 35 TRP cc_start: 0.7832 (m100) cc_final: 0.7584 (m-10) REVERT: A 78 ASP cc_start: 0.7859 (t0) cc_final: 0.7561 (p0) REVERT: A 102 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 103 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7734 (tp-100) REVERT: A 106 GLU cc_start: 0.8814 (tt0) cc_final: 0.8083 (tp30) REVERT: A 150 MET cc_start: 0.7862 (mmt) cc_final: 0.7086 (mmt) REVERT: A 168 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8120 (ttpt) REVERT: A 287 GLN cc_start: 0.7741 (tt0) cc_final: 0.7192 (mm-40) REVERT: A 340 GLU cc_start: 0.8827 (tt0) cc_final: 0.8619 (tt0) REVERT: A 486 TYR cc_start: 0.8814 (m-80) cc_final: 0.8002 (m-80) REVERT: B 535 MET cc_start: 0.8455 (mmm) cc_final: 0.8180 (mmm) REVERT: B 648 GLU cc_start: 0.7858 (tp30) cc_final: 0.7413 (tp30) REVERT: B 653 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.7004 (pp30) REVERT: C 97 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7758 (tptp) REVERT: C 112 TRP cc_start: 0.8378 (t-100) cc_final: 0.8081 (t-100) REVERT: C 177 TYR cc_start: 0.8442 (m-80) cc_final: 0.8061 (m-80) REVERT: C 210 PHE cc_start: 0.8343 (m-80) cc_final: 0.7828 (m-80) REVERT: C 492 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8331 (mt-10) REVERT: E 194 ILE cc_start: 0.8572 (tp) cc_final: 0.8250 (tt) REVERT: E 256 SER cc_start: 0.8862 (p) cc_final: 0.8561 (m) REVERT: E 426 MET cc_start: 0.8033 (tpt) cc_final: 0.7793 (tpt) REVERT: D 592 LEU cc_start: 0.8526 (tp) cc_final: 0.7877 (mt) REVERT: D 639 THR cc_start: 0.8563 (p) cc_final: 0.8022 (m) REVERT: F 543 ASN cc_start: 0.8497 (m-40) cc_final: 0.8016 (t0) REVERT: F 546 SER cc_start: 0.6809 (p) cc_final: 0.6437 (m) REVERT: F 647 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7908 (tm-30) outliers start: 56 outliers final: 35 residues processed: 310 average time/residue: 0.2777 time to fit residues: 126.8861 Evaluate side-chains 263 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 3.9990 chunk 127 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 170 optimal weight: 0.2980 chunk 180 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 543 ASN C 170 GLN C 289 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16323 Z= 0.261 Angle : 0.667 11.495 22180 Z= 0.335 Chirality : 0.048 0.281 2720 Planarity : 0.004 0.040 2735 Dihedral : 7.483 60.537 3652 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Rotamer: Outliers : 3.71 % Allowed : 13.58 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1867 helix: -0.01 (0.27), residues: 363 sheet: -0.16 (0.23), residues: 522 loop : -0.80 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 103 HIS 0.005 0.001 HIS A 216 PHE 0.019 0.002 PHE H 27 TYR 0.022 0.002 TYR A 217 ARG 0.005 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 246 time to evaluate : 1.740 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: H 78 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6995 (tp) REVERT: H 82 MET cc_start: 0.5842 (mmt) cc_final: 0.3885 (tpt) REVERT: H 100 ASP cc_start: 0.7323 (t0) cc_final: 0.7009 (t0) REVERT: H 100 TYR cc_start: 0.6161 (m-10) cc_final: 0.5601 (m-10) REVERT: L 38 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7470 (tp40) REVERT: L 42 GLN cc_start: 0.6111 (tp40) cc_final: 0.5717 (tp40) REVERT: L 82 ASP cc_start: 0.5111 (p0) cc_final: 0.4719 (p0) REVERT: A 35 TRP cc_start: 0.7865 (m100) cc_final: 0.7646 (m-10) REVERT: A 78 ASP cc_start: 0.7869 (t0) cc_final: 0.7561 (p0) REVERT: A 102 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 103 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7513 (tp-100) REVERT: A 150 MET cc_start: 0.7704 (mmt) cc_final: 0.6996 (mmt) REVERT: A 168 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8156 (ttpt) REVERT: A 287 GLN cc_start: 0.8048 (tt0) cc_final: 0.7325 (mm-40) REVERT: A 486 TYR cc_start: 0.8859 (m-80) cc_final: 0.7995 (m-80) REVERT: B 535 MET cc_start: 0.8441 (mmm) cc_final: 0.8219 (mmm) REVERT: B 648 GLU cc_start: 0.7805 (tp30) cc_final: 0.7572 (tp30) REVERT: B 653 GLN cc_start: 0.7588 (pp30) cc_final: 0.7295 (pp30) REVERT: C 97 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7669 (tptp) REVERT: C 112 TRP cc_start: 0.8307 (t-100) cc_final: 0.8105 (t-100) REVERT: C 168 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7581 (mtpt) REVERT: C 177 TYR cc_start: 0.8546 (m-80) cc_final: 0.8160 (m-80) REVERT: C 210 PHE cc_start: 0.8386 (m-80) cc_final: 0.7852 (m-80) REVERT: C 258 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: C 465 THR cc_start: 0.6154 (m) cc_final: 0.5761 (p) REVERT: C 492 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8415 (mt-10) REVERT: E 136 ASN cc_start: 0.8275 (m110) cc_final: 0.8043 (m110) REVERT: E 194 ILE cc_start: 0.8615 (tp) cc_final: 0.8241 (tt) REVERT: E 327 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7385 (mtm-85) REVERT: E 426 MET cc_start: 0.8035 (tpt) cc_final: 0.7831 (tpt) REVERT: D 592 LEU cc_start: 0.8643 (tp) cc_final: 0.8016 (mt) REVERT: D 639 THR cc_start: 0.8640 (p) cc_final: 0.8080 (m) REVERT: F 530 MET cc_start: 0.8361 (mtm) cc_final: 0.8071 (mtp) REVERT: F 543 ASN cc_start: 0.8498 (m-40) cc_final: 0.8042 (t0) REVERT: F 633 LYS cc_start: 0.9119 (tttm) cc_final: 0.8845 (mmmm) REVERT: F 647 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7951 (tm-30) outliers start: 62 outliers final: 42 residues processed: 286 average time/residue: 0.2743 time to fit residues: 116.8233 Evaluate side-chains 269 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN B 653 GLN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16323 Z= 0.246 Angle : 0.637 9.897 22180 Z= 0.322 Chirality : 0.047 0.299 2720 Planarity : 0.004 0.041 2735 Dihedral : 6.869 58.453 3651 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 4.01 % Allowed : 14.78 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1867 helix: 0.06 (0.28), residues: 366 sheet: -0.15 (0.23), residues: 490 loop : -0.86 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 103 HIS 0.005 0.001 HIS A 216 PHE 0.035 0.002 PHE H 29 TYR 0.017 0.002 TYR A 217 ARG 0.006 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 241 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7043 (tp) REVERT: H 82 MET cc_start: 0.5732 (mmt) cc_final: 0.3808 (tpt) REVERT: L 38 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7449 (tp40) REVERT: L 42 GLN cc_start: 0.6428 (tp40) cc_final: 0.6069 (tp40) REVERT: A 78 ASP cc_start: 0.7990 (t0) cc_final: 0.7623 (p0) REVERT: A 102 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7413 (tm-30) REVERT: A 103 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7578 (tp-100) REVERT: A 150 MET cc_start: 0.7783 (mmt) cc_final: 0.7147 (mmt) REVERT: A 168 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8309 (ttpt) REVERT: A 426 MET cc_start: 0.7304 (ttp) cc_final: 0.5905 (tpt) REVERT: A 486 TYR cc_start: 0.8812 (m-80) cc_final: 0.7832 (m-80) REVERT: B 647 GLU cc_start: 0.7639 (tp30) cc_final: 0.6536 (tp30) REVERT: C 97 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7409 (tptp) REVERT: C 168 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7659 (mtpt) REVERT: C 177 TYR cc_start: 0.8575 (m-80) cc_final: 0.8187 (m-80) REVERT: C 210 PHE cc_start: 0.8400 (m-80) cc_final: 0.7884 (m-80) REVERT: C 258 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: C 465 THR cc_start: 0.5880 (m) cc_final: 0.5536 (p) REVERT: E 213 ILE cc_start: 0.8281 (tt) cc_final: 0.8041 (tp) REVERT: E 426 MET cc_start: 0.8087 (tpt) cc_final: 0.7866 (tpt) REVERT: D 530 MET cc_start: 0.8833 (ttp) cc_final: 0.8495 (ttp) REVERT: D 592 LEU cc_start: 0.8661 (tp) cc_final: 0.8182 (mt) REVERT: D 639 THR cc_start: 0.8641 (p) cc_final: 0.8129 (m) REVERT: F 530 MET cc_start: 0.8361 (mtm) cc_final: 0.8046 (mtp) REVERT: F 633 LYS cc_start: 0.9085 (tttm) cc_final: 0.8851 (mmmm) REVERT: F 647 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7880 (tm-30) outliers start: 67 outliers final: 43 residues processed: 284 average time/residue: 0.2780 time to fit residues: 117.7923 Evaluate side-chains 269 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.0970 chunk 162 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 59 optimal weight: 0.0050 chunk 94 optimal weight: 0.3980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN B 653 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16323 Z= 0.188 Angle : 0.607 9.747 22180 Z= 0.308 Chirality : 0.046 0.313 2720 Planarity : 0.004 0.048 2735 Dihedral : 6.325 58.044 3651 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 3.41 % Allowed : 15.80 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 1867 helix: 0.35 (0.28), residues: 354 sheet: -0.24 (0.23), residues: 500 loop : -0.78 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP H 103 HIS 0.004 0.001 HIS C 374 PHE 0.048 0.002 PHE D 522 TYR 0.024 0.002 TYR A 484 ARG 0.006 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 250 time to evaluate : 1.877 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: H 82 MET cc_start: 0.5769 (mmt) cc_final: 0.3906 (tpt) REVERT: H 100 ASP cc_start: 0.7173 (t0) cc_final: 0.6817 (t0) REVERT: H 100 TYR cc_start: 0.6724 (m-10) cc_final: 0.6472 (m-10) REVERT: L 38 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7438 (tp40) REVERT: L 42 GLN cc_start: 0.6660 (tp40) cc_final: 0.6357 (tp40) REVERT: A 103 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7708 (tp-100) REVERT: A 150 MET cc_start: 0.7779 (mmt) cc_final: 0.7189 (mmt) REVERT: A 168 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8321 (ttpt) REVERT: A 426 MET cc_start: 0.7127 (ttp) cc_final: 0.5848 (tpt) REVERT: A 457 ASP cc_start: 0.7774 (m-30) cc_final: 0.7567 (m-30) REVERT: A 486 TYR cc_start: 0.8686 (m-80) cc_final: 0.7704 (m-80) REVERT: B 648 GLU cc_start: 0.7540 (tp30) cc_final: 0.7250 (tp30) REVERT: B 653 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6567 (pp30) REVERT: C 97 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7306 (tptp) REVERT: C 132 THR cc_start: 0.9291 (p) cc_final: 0.9034 (t) REVERT: C 168 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7649 (mtpt) REVERT: C 177 TYR cc_start: 0.8502 (m-80) cc_final: 0.8101 (m-80) REVERT: C 210 PHE cc_start: 0.8395 (m-80) cc_final: 0.7868 (m-80) REVERT: C 258 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: C 465 THR cc_start: 0.5665 (m) cc_final: 0.5371 (p) REVERT: E 426 MET cc_start: 0.8080 (tpt) cc_final: 0.7822 (tpt) REVERT: D 530 MET cc_start: 0.8769 (ttp) cc_final: 0.8486 (ttp) REVERT: D 592 LEU cc_start: 0.8682 (tp) cc_final: 0.8207 (mt) REVERT: F 633 LYS cc_start: 0.9076 (tttm) cc_final: 0.8841 (mmmm) REVERT: F 647 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7855 (tm-30) outliers start: 57 outliers final: 45 residues processed: 283 average time/residue: 0.2818 time to fit residues: 117.8332 Evaluate side-chains 281 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 233 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 0.2980 chunk 20 optimal weight: 40.0000 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16323 Z= 0.291 Angle : 0.644 9.351 22180 Z= 0.328 Chirality : 0.048 0.315 2720 Planarity : 0.004 0.041 2735 Dihedral : 6.450 56.267 3648 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 3.29 % Allowed : 16.40 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1867 helix: 0.39 (0.29), residues: 354 sheet: -0.48 (0.23), residues: 515 loop : -0.81 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 103 HIS 0.006 0.001 HIS A 216 PHE 0.026 0.002 PHE D 522 TYR 0.027 0.002 TYR A 484 ARG 0.007 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 248 time to evaluate : 1.744 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: H 82 MET cc_start: 0.5798 (mmt) cc_final: 0.3978 (tpt) REVERT: H 100 ASP cc_start: 0.8882 (p0) cc_final: 0.8630 (p0) REVERT: H 100 ASP cc_start: 0.7248 (t0) cc_final: 0.6860 (t0) REVERT: H 100 TYR cc_start: 0.6578 (m-10) cc_final: 0.6005 (m-10) REVERT: L 38 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7515 (tp40) REVERT: L 42 GLN cc_start: 0.6778 (tp40) cc_final: 0.6452 (tp40) REVERT: A 102 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 103 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8002 (tp-100) REVERT: A 150 MET cc_start: 0.7810 (mmt) cc_final: 0.7240 (mmt) REVERT: A 168 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8396 (ttpt) REVERT: A 426 MET cc_start: 0.7451 (ttp) cc_final: 0.6025 (tpt) REVERT: A 486 TYR cc_start: 0.8812 (m-80) cc_final: 0.7847 (m-80) REVERT: B 542 ARG cc_start: 0.8584 (ttm-80) cc_final: 0.8380 (ttm-80) REVERT: B 647 GLU cc_start: 0.7854 (tp30) cc_final: 0.7264 (tp30) REVERT: B 648 GLU cc_start: 0.7520 (tp30) cc_final: 0.7181 (tp30) REVERT: B 653 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6832 (pp30) REVERT: C 97 LYS cc_start: 0.7679 (mmtt) cc_final: 0.7336 (tptp) REVERT: C 168 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7711 (mtpt) REVERT: C 177 TYR cc_start: 0.8590 (m-80) cc_final: 0.8261 (m-80) REVERT: C 210 PHE cc_start: 0.8436 (m-80) cc_final: 0.7919 (m-80) REVERT: C 258 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: C 465 THR cc_start: 0.5741 (m) cc_final: 0.5391 (p) REVERT: E 452 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8859 (mt) REVERT: D 639 THR cc_start: 0.8626 (p) cc_final: 0.8181 (m) REVERT: F 633 LYS cc_start: 0.9082 (tttm) cc_final: 0.8848 (mmmm) REVERT: F 647 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7710 (tm-30) outliers start: 55 outliers final: 45 residues processed: 281 average time/residue: 0.2782 time to fit residues: 116.3930 Evaluate side-chains 282 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 233 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100HHIS A 103 GLN B 653 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16323 Z= 0.231 Angle : 0.618 10.688 22180 Z= 0.314 Chirality : 0.047 0.384 2720 Planarity : 0.004 0.041 2735 Dihedral : 6.254 56.704 3648 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 3.59 % Allowed : 16.22 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1867 helix: 0.46 (0.29), residues: 354 sheet: -0.51 (0.23), residues: 515 loop : -0.83 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 103 HIS 0.004 0.001 HIS E 216 PHE 0.020 0.002 PHE D 522 TYR 0.027 0.002 TYR A 484 ARG 0.005 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 237 time to evaluate : 1.782 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: H 82 MET cc_start: 0.5742 (mmt) cc_final: 0.3863 (tpt) REVERT: L 38 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7547 (tp40) REVERT: L 42 GLN cc_start: 0.6853 (tp40) cc_final: 0.6555 (tp40) REVERT: A 103 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8145 (tp-100) REVERT: A 104 MET cc_start: 0.7670 (ttp) cc_final: 0.6730 (ttp) REVERT: A 150 MET cc_start: 0.7842 (mmt) cc_final: 0.7359 (mmt) REVERT: A 168 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8404 (ttpt) REVERT: A 426 MET cc_start: 0.7329 (ttp) cc_final: 0.5748 (tpt) REVERT: A 486 TYR cc_start: 0.8722 (m-80) cc_final: 0.7756 (m-80) REVERT: B 647 GLU cc_start: 0.7832 (tp30) cc_final: 0.7271 (tp30) REVERT: B 648 GLU cc_start: 0.7522 (tp30) cc_final: 0.7179 (tp30) REVERT: B 653 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6810 (pp30) REVERT: C 97 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7264 (tptp) REVERT: C 168 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7704 (mtpt) REVERT: C 177 TYR cc_start: 0.8553 (m-80) cc_final: 0.8223 (m-80) REVERT: C 210 PHE cc_start: 0.8433 (m-80) cc_final: 0.7910 (m-80) REVERT: C 258 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: C 465 THR cc_start: 0.5891 (m) cc_final: 0.5524 (p) REVERT: E 295 ASN cc_start: 0.6782 (m-40) cc_final: 0.6273 (m-40) REVERT: D 650 GLN cc_start: 0.6804 (tm-30) cc_final: 0.6564 (tm-30) REVERT: F 633 LYS cc_start: 0.9093 (tttm) cc_final: 0.8863 (mmmm) REVERT: F 647 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7745 (tm-30) outliers start: 60 outliers final: 49 residues processed: 269 average time/residue: 0.2727 time to fit residues: 109.8085 Evaluate side-chains 280 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 228 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 167 optimal weight: 0.0770 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 151 optimal weight: 0.4980 chunk 158 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 653 GLN C 249 HIS C 287 GLN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 249 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16323 Z= 0.180 Angle : 0.589 10.652 22180 Z= 0.301 Chirality : 0.046 0.332 2720 Planarity : 0.004 0.041 2735 Dihedral : 6.060 56.796 3648 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 2.93 % Allowed : 16.76 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1867 helix: 0.52 (0.29), residues: 354 sheet: -0.44 (0.24), residues: 501 loop : -0.84 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP H 47 HIS 0.005 0.001 HIS C 374 PHE 0.017 0.001 PHE D 522 TYR 0.024 0.002 TYR A 484 ARG 0.005 0.000 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 228 time to evaluate : 1.754 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: H 82 MET cc_start: 0.5765 (mmt) cc_final: 0.3851 (tpt) REVERT: L 38 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7536 (tp40) REVERT: L 42 GLN cc_start: 0.6890 (tp40) cc_final: 0.6602 (tp40) REVERT: A 78 ASP cc_start: 0.7862 (t0) cc_final: 0.7660 (p0) REVERT: A 103 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8201 (tp-100) REVERT: A 150 MET cc_start: 0.7790 (mmt) cc_final: 0.7240 (mmt) REVERT: A 168 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8502 (ttpt) REVERT: A 426 MET cc_start: 0.7254 (ttp) cc_final: 0.5731 (tpt) REVERT: A 486 TYR cc_start: 0.8610 (m-80) cc_final: 0.7831 (m-80) REVERT: B 647 GLU cc_start: 0.7814 (tp30) cc_final: 0.7261 (tp30) REVERT: B 653 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6878 (pp30) REVERT: C 97 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7238 (tptp) REVERT: C 132 THR cc_start: 0.9211 (p) cc_final: 0.8945 (t) REVERT: C 168 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7706 (mtpt) REVERT: C 210 PHE cc_start: 0.8419 (m-80) cc_final: 0.7896 (m-80) REVERT: C 287 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: C 465 THR cc_start: 0.5772 (m) cc_final: 0.5398 (p) REVERT: E 295 ASN cc_start: 0.6696 (m-40) cc_final: 0.6288 (m-40) REVERT: E 352 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.7327 (t-90) REVERT: F 633 LYS cc_start: 0.9092 (tttm) cc_final: 0.8863 (mmmm) REVERT: F 647 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7697 (tm-30) outliers start: 49 outliers final: 40 residues processed: 258 average time/residue: 0.2749 time to fit residues: 105.8438 Evaluate side-chains 258 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 214 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 0.0770 chunk 108 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 653 GLN C 287 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16323 Z= 0.201 Angle : 0.613 12.597 22180 Z= 0.312 Chirality : 0.046 0.254 2720 Planarity : 0.004 0.068 2735 Dihedral : 6.012 56.209 3648 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 3.11 % Allowed : 17.30 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1867 helix: 0.61 (0.29), residues: 354 sheet: -0.42 (0.24), residues: 501 loop : -0.84 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP H 47 HIS 0.007 0.001 HIS C 249 PHE 0.019 0.002 PHE D 522 TYR 0.032 0.002 TYR F 643 ARG 0.011 0.001 ARG B 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 219 time to evaluate : 1.612 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: H 82 MET cc_start: 0.5873 (mmt) cc_final: 0.3918 (tpt) REVERT: L 38 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7553 (tp40) REVERT: L 42 GLN cc_start: 0.6899 (tp40) cc_final: 0.6603 (tp40) REVERT: A 78 ASP cc_start: 0.7916 (t0) cc_final: 0.7657 (p0) REVERT: A 103 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8264 (tp-100) REVERT: A 150 MET cc_start: 0.7871 (mmt) cc_final: 0.7326 (mmt) REVERT: A 168 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8616 (ttpt) REVERT: A 426 MET cc_start: 0.7272 (ttp) cc_final: 0.5726 (tpp) REVERT: A 486 TYR cc_start: 0.8652 (m-80) cc_final: 0.7872 (m-80) REVERT: B 647 GLU cc_start: 0.7774 (tp30) cc_final: 0.7236 (tp30) REVERT: B 653 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7066 (pp30) REVERT: C 97 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7245 (tptp) REVERT: C 132 THR cc_start: 0.9187 (p) cc_final: 0.8922 (t) REVERT: C 168 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7716 (mtmt) REVERT: C 210 PHE cc_start: 0.8426 (m-80) cc_final: 0.7905 (m-80) REVERT: C 287 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: C 465 THR cc_start: 0.5982 (m) cc_final: 0.5589 (p) REVERT: E 295 ASN cc_start: 0.6672 (m-40) cc_final: 0.6246 (m-40) REVERT: E 352 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7453 (t-90) REVERT: D 625 ASN cc_start: 0.8251 (t0) cc_final: 0.7963 (t0) REVERT: F 633 LYS cc_start: 0.9099 (tttm) cc_final: 0.8872 (mmmm) REVERT: F 647 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7784 (tm-30) outliers start: 52 outliers final: 44 residues processed: 251 average time/residue: 0.2620 time to fit residues: 98.6683 Evaluate side-chains 259 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.156389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121591 restraints weight = 24408.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121975 restraints weight = 26810.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123494 restraints weight = 22129.884| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 16323 Z= 0.322 Angle : 0.917 59.156 22180 Z= 0.534 Chirality : 0.051 1.167 2720 Planarity : 0.005 0.113 2735 Dihedral : 6.019 56.198 3648 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.14 % Rotamer: Outliers : 2.99 % Allowed : 17.77 % Favored : 79.23 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1867 helix: 0.58 (0.29), residues: 354 sheet: -0.42 (0.24), residues: 501 loop : -0.86 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP H 47 HIS 0.007 0.001 HIS C 249 PHE 0.018 0.002 PHE E 53 TYR 0.026 0.002 TYR F 643 ARG 0.011 0.000 ARG L 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3305.20 seconds wall clock time: 59 minutes 53.88 seconds (3593.88 seconds total)