Starting phenix.real_space_refine (version: dev) on Wed Apr 6 04:12:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/04_2022/7mo7_23919_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/04_2022/7mo7_23919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/04_2022/7mo7_23919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/04_2022/7mo7_23919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/04_2022/7mo7_23919_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo7_23919/04_2022/7mo7_23919_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 18135 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2287 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 Chain: "E" Number of atoms: 5324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5324 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 31, 'TRANS': 654, 'PCIS': 2} Chain breaks: 4 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 4937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4937 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 38, 'TRANS': 595, 'PCIS': 3} Chain breaks: 6 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 154 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 5490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5490 Classifications: {'peptide': 699} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 31, 'TRANS': 665, 'PCIS': 2} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {'IDS': 3, 'SGN': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 10.52, per 1000 atoms: 0.58 Number of scatterers: 18135 At special positions: 0 Unit cell: (154.44, 181.44, 168.48, 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 161 16.00 O 3416 8.00 N 3128 7.00 C 11430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 469 " distance=2.03 Simple disulfide: pdb=" SG CYS D 412 " - pdb=" SG CYS D 452 " distance=2.03 Simple disulfide: pdb=" SG CYS D 440 " - pdb=" SG CYS D 464 " distance=2.03 Simple disulfide: pdb=" SG CYS D 519 " - pdb=" SG CYS D 535 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 679 " distance=2.04 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 658 " distance=2.03 Simple disulfide: pdb=" SG CYS D 669 " - pdb=" SG CYS D 697 " distance=2.04 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 584 " distance=2.03 Simple disulfide: pdb=" SG CYS E 95 " - pdb=" SG CYS E 101 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 160 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 409 " distance=2.04 Simple disulfide: pdb=" SG CYS E 298 " - pdb=" SG CYS E 363 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 397 " distance=2.03 Simple disulfide: pdb=" SG CYS E 520 " - pdb=" SG CYS E 538 " distance=2.03 Simple disulfide: pdb=" SG CYS E 526 " - pdb=" SG CYS E 561 " distance=2.02 Simple disulfide: pdb=" SG CYS E 529 " - pdb=" SG CYS E 545 " distance=2.03 Simple disulfide: pdb=" SG CYS E 541 " - pdb=" SG CYS E 551 " distance=2.03 Simple disulfide: pdb=" SG CYS E 610 " - pdb=" SG CYS E 624 " distance=2.03 Simple disulfide: pdb=" SG CYS E 697 " - pdb=" SG CYS E 709 " distance=2.04 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 377 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 469 " distance=2.03 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 452 " distance=2.03 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 464 " distance=2.03 Simple disulfide: pdb=" SG CYS A 519 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 679 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 160 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 397 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 538 " distance=2.03 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 610 " - pdb=" SG CYS B 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 709 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 ALPHA1-4 " IDS F 2 " - " SGN F 3 " " IDS F 4 " - " SGN F 5 " BETA1-4 " SGN F 1 " - " IDS F 2 " ~> Even though IDS is an alpha isomer, a beta linkage is required... " SGN F 3 " - " IDS F 4 " " SGN F 5 " - " IDS F 6 " Time building additional restraints: 7.31 Conformation dependent library (CDL) restraints added in 2.7 seconds 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 39 sheets defined 8.1% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 415 through 425 Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 639 through 646 Processing helix chain 'D' and resid 709 through 720 removed outlier: 4.168A pdb=" N LYS D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP D 715 " --> pdb=" O TYR D 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 203 through 208 Proline residue: E 207 - end of helix No H-bonds generated for 'chain 'E' and resid 203 through 208' Processing helix chain 'E' and resid 231 through 233 No H-bonds generated for 'chain 'E' and resid 231 through 233' Processing helix chain 'E' and resid 239 through 241 No H-bonds generated for 'chain 'E' and resid 239 through 241' Processing helix chain 'E' and resid 327 through 332 removed outlier: 3.765A pdb=" N ARG E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN E 332 " --> pdb=" O GLN E 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 327 through 332' Processing helix chain 'E' and resid 367 through 375 Processing helix chain 'E' and resid 387 through 390 No H-bonds generated for 'chain 'E' and resid 387 through 390' Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 526 through 531 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 639 through 645 Processing helix chain 'A' and resid 709 through 711 No H-bonds generated for 'chain 'A' and resid 709 through 711' Processing helix chain 'A' and resid 713 through 721 removed outlier: 4.115A pdb=" N LEU A 721 " --> pdb=" O HIS A 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 367 through 375 Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 396 through 399 No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing sheet with id= A, first strand: chain 'D' and resid 451 through 453 Processing sheet with id= B, first strand: chain 'D' and resid 563 through 565 removed outlier: 4.186A pdb=" N CYS D 519 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR D 513 " --> pdb=" O HIS D 517 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N HIS D 517 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLY D 520 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA D 532 " --> pdb=" O GLY D 520 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 611 through 616 Processing sheet with id= D, first strand: chain 'D' and resid 656 through 659 removed outlier: 6.652A pdb=" N LEU D 677 " --> pdb=" O LEU D 688 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= F, first strand: chain 'E' and resid 52 through 58 removed outlier: 6.726A pdb=" N GLY E 65 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL E 55 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE E 63 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU E 57 " --> pdb=" O HIS E 61 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 82 " --> pdb=" O VAL E 72 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 89 through 91 Processing sheet with id= H, first strand: chain 'E' and resid 119 through 123 removed outlier: 4.033A pdb=" N ALA E 119 " --> pdb=" O CYS E 133 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS E 141 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 182 through 188 Processing sheet with id= J, first strand: chain 'E' and resid 424 through 427 removed outlier: 4.256A pdb=" N THR E 276 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N CYS E 298 " --> pdb=" O PHE E 274 " (cutoff:3.500A) removed outlier: 13.541A pdb=" N PHE E 274 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE E 281 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL E 264 " --> pdb=" O TYR E 249 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR E 249 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 298 through 300 removed outlier: 4.001A pdb=" N CYS E 298 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 477 through 480 removed outlier: 3.609A pdb=" N VAL E 477 " --> pdb=" O GLN E 464 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG E 461 " --> pdb=" O THR E 457 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 441 " --> pdb=" O GLY E 456 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 538 through 540 Processing sheet with id= N, first strand: chain 'E' and resid 621 through 625 removed outlier: 6.561A pdb=" N TRP E 586 " --> pdb=" O ILE E 565 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE E 565 " --> pdb=" O TRP E 586 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 601 through 605 Processing sheet with id= P, first strand: chain 'E' and resid 658 through 663 removed outlier: 6.905A pdb=" N THR E 678 " --> pdb=" O THR E 660 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE E 662 " --> pdb=" O THR E 676 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR E 676 " --> pdb=" O ILE E 662 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR E 710 " --> pdb=" O LEU E 699 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU E 699 " --> pdb=" O TYR E 710 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 316 through 324 removed outlier: 6.771A pdb=" N VAL E 345 " --> pdb=" O GLN E 318 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA E 320 " --> pdb=" O PHE E 343 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE E 343 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL E 322 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE E 341 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG E 359 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 49 through 52 Processing sheet with id= S, first strand: chain 'A' and resid 61 through 63 removed outlier: 3.519A pdb=" N GLN A 95 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 90 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 188 through 190 Processing sheet with id= U, first strand: chain 'A' and resid 270 through 272 Processing sheet with id= V, first strand: chain 'A' and resid 451 through 453 Processing sheet with id= W, first strand: chain 'A' and resid 563 through 565 removed outlier: 8.112A pdb=" N GLY A 520 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA A 532 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 612 through 616 Processing sheet with id= Y, first strand: chain 'A' and resid 656 through 659 Processing sheet with id= Z, first strand: chain 'A' and resid 676 through 680 removed outlier: 5.865A pdb=" N CYS A 679 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 687 " --> pdb=" O CYS A 679 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 44 through 47 Processing sheet with id= AB, first strand: chain 'B' and resid 52 through 58 removed outlier: 7.052A pdb=" N GLY B 65 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL B 55 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 63 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B 57 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 82 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN B 74 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS B 80 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 121 through 123 Processing sheet with id= AD, first strand: chain 'B' and resid 181 through 189 Processing sheet with id= AE, first strand: chain 'B' and resid 424 through 427 removed outlier: 4.511A pdb=" N THR B 276 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 281 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 259 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 264 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TYR B 249 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 298 through 300 removed outlier: 4.018A pdb=" N CYS B 298 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 360 through 366 removed outlier: 3.754A pdb=" N ALA B 319 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA B 347 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU B 317 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 383 through 385 Processing sheet with id= AI, first strand: chain 'B' and resid 463 through 467 removed outlier: 4.775A pdb=" N THR B 451 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 621 through 624 removed outlier: 6.376A pdb=" N TRP B 586 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE B 565 " --> pdb=" O TRP B 586 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 602 through 604 Processing sheet with id= AL, first strand: chain 'B' and resid 674 through 678 removed outlier: 3.507A pdb=" N CYS B 709 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR B 710 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU B 699 " --> pdb=" O TYR B 710 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 689 through 691 397 hydrogen bonds defined for protein. 1053 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: 6.00 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5913 1.34 - 1.46: 4347 1.46 - 1.58: 8116 1.58 - 1.71: 3 1.71 - 1.83: 195 Bond restraints: 18574 Sorted by residual: bond pdb=" O6 SGN F 1 " pdb=" S2 SGN F 1 " ideal model delta sigma weight residual 1.660 1.526 0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" O6 SGN F 3 " pdb=" S2 SGN F 3 " ideal model delta sigma weight residual 1.660 1.527 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" O2 IDS F 6 " pdb=" S IDS F 6 " ideal model delta sigma weight residual 1.651 1.529 0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" O2 IDS F 2 " pdb=" S IDS F 2 " ideal model delta sigma weight residual 1.651 1.536 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" O2 IDS F 4 " pdb=" S IDS F 4 " ideal model delta sigma weight residual 1.651 1.539 0.112 2.00e-02 2.50e+03 3.15e+01 ... (remaining 18569 not shown) Histogram of bond angle deviations from ideal: 98.00 - 105.21: 396 105.21 - 112.43: 9471 112.43 - 119.64: 6007 119.64 - 126.85: 9083 126.85 - 134.07: 291 Bond angle restraints: 25248 Sorted by residual: angle pdb=" C2 SGN F 1 " pdb=" N SGN F 1 " pdb=" S1 SGN F 1 " ideal model delta sigma weight residual 119.97 106.49 13.48 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C LEU D 523 " pdb=" N ILE D 524 " pdb=" CA ILE D 524 " ideal model delta sigma weight residual 123.08 119.49 3.59 1.01e+00 9.80e-01 1.26e+01 angle pdb=" C2 SGN F 3 " pdb=" N SGN F 3 " pdb=" S1 SGN F 3 " ideal model delta sigma weight residual 119.97 109.35 10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C ILE B 726 " pdb=" N ASP B 727 " pdb=" CA ASP B 727 " ideal model delta sigma weight residual 121.54 127.89 -6.35 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C SER B 684 " pdb=" N GLY B 685 " pdb=" CA GLY B 685 " ideal model delta sigma weight residual 121.85 117.94 3.91 1.24e+00 6.50e-01 9.96e+00 ... (remaining 25243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9966 17.94 - 35.88: 946 35.88 - 53.81: 154 53.81 - 71.75: 40 71.75 - 89.69: 21 Dihedral angle restraints: 11127 sinusoidal: 4395 harmonic: 6732 Sorted by residual: dihedral pdb=" CB CYS A 177 " pdb=" SG CYS A 177 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual 93.00 -177.31 -89.69 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS D 412 " pdb=" SG CYS D 412 " pdb=" SG CYS D 452 " pdb=" CB CYS D 452 " ideal model delta sinusoidal sigma weight residual 93.00 179.99 -86.99 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS A 305 " pdb=" SG CYS A 305 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual -86.00 -165.50 79.50 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 11124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2157 0.050 - 0.099: 497 0.099 - 0.149: 142 0.149 - 0.198: 6 0.198 - 0.248: 2 Chirality restraints: 2804 Sorted by residual: chirality pdb=" C1 SGN F 3 " pdb=" O4 IDS F 2 " pdb=" C2 SGN F 3 " pdb=" O5 SGN F 3 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 1.90e+01 chirality pdb=" C1 IDS F 2 " pdb=" O4 SGN F 1 " pdb=" C2 IDS F 2 " pdb=" O5 IDS F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.79e+01 chirality pdb=" C1 IDS F 4 " pdb=" O4 SGN F 3 " pdb=" C2 IDS F 4 " pdb=" O5 IDS F 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.31e+00 ... (remaining 2801 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 442 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 443 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 443 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 443 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 459 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 460 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 569 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO E 570 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 570 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 570 " 0.023 5.00e-02 4.00e+02 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 555 2.68 - 3.24: 18390 3.24 - 3.79: 29109 3.79 - 4.35: 38952 4.35 - 4.90: 61101 Nonbonded interactions: 148107 Sorted by model distance: nonbonded pdb=" O THR E 230 " pdb=" OG SER E 233 " model vdw 2.126 2.440 nonbonded pdb=" O SER B 684 " pdb=" NH2 ARG B 688 " model vdw 2.150 2.520 nonbonded pdb=" OG1 THR D 454 " pdb=" O ILE D 459 " model vdw 2.154 2.440 nonbonded pdb=" N TYR E 566 " pdb=" O CYS E 584 " model vdw 2.164 2.520 nonbonded pdb=" OG1 THR A 38 " pdb=" OG1 THR A 75 " model vdw 2.166 2.440 ... (remaining 148102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 26 through 106 or resid 111 through 301 or resid 311 throu \ gh 664 or (resid 665 through 666 and (name N or name CA or name C or name O or n \ ame CB )) or resid 667 through 668 or (resid 669 through 670 and (name N or name \ CA or name C or name O or name CB )) or resid 671 through 680 or (resid 687 thr \ ough 689 and (name N or name CA or name C or name O or name CB )) or resid 690 t \ hrough 694 or (resid 695 and (name N or name CA or name C or name O or name CB ) \ ) or resid 696 through 699 or (resid 700 and (name N or name CA or name C or nam \ e O or name CB )) or resid 701 through 707 or (resid 708 and (name N or name CA \ or name C or name O or name CB )) or resid 709 or (resid 710 and (name N or name \ CA or name C or name O or name CB )) or resid 711 through 718 or (resid 719 and \ (name N or name CA or name C or name O or name CB )) or resid 720 through 722 o \ r (resid 723 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 24 or (resid 725 and (name N or name CA or name C or name O or name CB )) or res \ id 726 through 730 or (resid 731 through 732 and (name N or name CA or name C or \ name O or name CB )) or resid 733 through 738)) selection = (chain 'E' and (resid 26 through 106 or resid 111 through 738)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 161 5.16 5 C 11430 2.51 5 N 3128 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.970 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: 5.730 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.130 Process input model: 47.330 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.004 0.134 18574 Z= 0.295 Angle : 0.735 13.482 25248 Z= 0.392 Chirality : 0.046 0.248 2804 Planarity : 0.004 0.056 3256 Dihedral : 14.045 88.668 6636 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.19 (0.17), residues: 2291 helix: -0.57 (0.44), residues: 148 sheet: -0.19 (0.22), residues: 517 loop : -1.06 (0.15), residues: 1626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2831 time to fit residues: 50.3642 Evaluate side-chains 72 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 59 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 chunk 180 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 448 HIS ** D 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 18574 Z= 0.353 Angle : 0.718 8.521 25248 Z= 0.374 Chirality : 0.047 0.240 2804 Planarity : 0.005 0.048 3256 Dihedral : 6.007 52.841 2506 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 29.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.41 (0.17), residues: 2291 helix: -0.98 (0.42), residues: 150 sheet: -0.49 (0.22), residues: 526 loop : -1.13 (0.15), residues: 1615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.2804 time to fit residues: 39.4645 Evaluate side-chains 65 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1751 time to fit residues: 3.4577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 173 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 226 optimal weight: 50.0000 chunk 186 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS E 199 ASN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 18574 Z= 0.269 Angle : 0.637 8.940 25248 Z= 0.331 Chirality : 0.046 0.213 2804 Planarity : 0.005 0.058 3256 Dihedral : 5.867 51.351 2506 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.33 (0.17), residues: 2291 helix: -0.81 (0.42), residues: 150 sheet: -0.48 (0.22), residues: 530 loop : -1.06 (0.16), residues: 1611 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.075 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2624 time to fit residues: 35.9655 Evaluate side-chains 64 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 209 optimal weight: 8.9990 chunk 222 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 chunk 59 optimal weight: 0.0970 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 418 ASN ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 ASN E 494 HIS ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 18574 Z= 0.222 Angle : 0.604 9.021 25248 Z= 0.311 Chirality : 0.045 0.209 2804 Planarity : 0.004 0.062 3256 Dihedral : 5.660 50.884 2506 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.26 (0.17), residues: 2291 helix: -0.82 (0.42), residues: 156 sheet: -0.38 (0.22), residues: 536 loop : -1.03 (0.16), residues: 1599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2773 time to fit residues: 37.0662 Evaluate side-chains 63 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.068 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 113 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 534 GLN D 681 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 18574 Z= 0.319 Angle : 0.682 11.314 25248 Z= 0.355 Chirality : 0.047 0.289 2804 Planarity : 0.005 0.051 3256 Dihedral : 5.933 49.518 2506 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 29.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.41 (0.17), residues: 2291 helix: -0.98 (0.42), residues: 147 sheet: -0.58 (0.22), residues: 541 loop : -1.10 (0.16), residues: 1603 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 0.2652 time to fit residues: 35.3242 Evaluate side-chains 63 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1593 time to fit residues: 3.1791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 0.9990 chunk 200 optimal weight: 0.0000 chunk 43 optimal weight: 0.0770 chunk 130 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 222 optimal weight: 50.0000 chunk 184 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 0.0670 chunk 73 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.8284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 681 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 HIS ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 18574 Z= 0.170 Angle : 0.593 9.423 25248 Z= 0.304 Chirality : 0.046 0.209 2804 Planarity : 0.004 0.044 3256 Dihedral : 5.475 48.718 2506 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.23 (0.17), residues: 2291 helix: -0.70 (0.42), residues: 156 sheet: -0.36 (0.22), residues: 525 loop : -1.02 (0.16), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2955 time to fit residues: 41.7147 Evaluate side-chains 64 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 221 optimal weight: 40.0000 chunk 138 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 484 HIS ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 18574 Z= 0.244 Angle : 0.615 9.008 25248 Z= 0.319 Chirality : 0.045 0.205 2804 Planarity : 0.005 0.054 3256 Dihedral : 5.557 47.984 2506 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.26 (0.18), residues: 2291 helix: -0.81 (0.43), residues: 150 sheet: -0.44 (0.22), residues: 532 loop : -1.01 (0.16), residues: 1609 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2755 time to fit residues: 37.2418 Evaluate side-chains 62 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 2.028 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 chunk 174 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 601 ASN D 681 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 18574 Z= 0.379 Angle : 0.759 12.065 25248 Z= 0.398 Chirality : 0.048 0.212 2804 Planarity : 0.006 0.054 3256 Dihedral : 6.327 47.662 2506 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 35.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.66 (0.17), residues: 2291 helix: -1.56 (0.40), residues: 146 sheet: -0.73 (0.22), residues: 535 loop : -1.23 (0.16), residues: 1610 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2683 time to fit residues: 34.2445 Evaluate side-chains 60 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 2.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 2.9990 chunk 212 optimal weight: 0.1980 chunk 193 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 681 GLN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 18574 Z= 0.186 Angle : 0.623 9.398 25248 Z= 0.319 Chirality : 0.047 0.381 2804 Planarity : 0.004 0.049 3256 Dihedral : 5.723 47.152 2506 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.39 (0.17), residues: 2291 helix: -1.21 (0.41), residues: 162 sheet: -0.48 (0.23), residues: 500 loop : -1.08 (0.16), residues: 1629 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2860 time to fit residues: 38.8198 Evaluate side-chains 62 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 2.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 0.6980 chunk 218 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 103 optimal weight: 0.0270 chunk 151 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 overall best weight: 2.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 717 HIS ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 18574 Z= 0.190 Angle : 0.604 9.152 25248 Z= 0.309 Chirality : 0.046 0.310 2804 Planarity : 0.004 0.046 3256 Dihedral : 5.529 46.453 2506 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.35 (0.17), residues: 2291 helix: -1.15 (0.41), residues: 165 sheet: -0.51 (0.22), residues: 511 loop : -1.03 (0.16), residues: 1615 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3093 time to fit residues: 40.6812 Evaluate side-chains 63 residues out of total 2075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 528 GLN B 53 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.036804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.028244 restraints weight = 285131.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.029045 restraints weight = 179472.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.029593 restraints weight = 127306.501| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 18574 Z= 0.154 Angle : 0.586 8.813 25248 Z= 0.296 Chirality : 0.046 0.307 2804 Planarity : 0.004 0.063 3256 Dihedral : 5.165 46.080 2506 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % 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: -1.19 (0.17), residues: 2291 helix: -0.94 (0.41), residues: 165 sheet: -0.24 (0.23), residues: 502 loop : -0.99 (0.16), residues: 1624 =============================================================================== Job complete usr+sys time: 2483.84 seconds wall clock time: 48 minutes 24.96 seconds (2904.96 seconds total)