Starting phenix.real_space_refine on Fri Dec 15 01:42:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja8_6338/12_2023/3ja8_6338_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja8_6338/12_2023/3ja8_6338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja8_6338/12_2023/3ja8_6338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja8_6338/12_2023/3ja8_6338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja8_6338/12_2023/3ja8_6338_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3ja8_6338/12_2023/3ja8_6338_neut_updated.pdb" } resolution = 3.8 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= -0.058 sd= 0.697 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 132 5.16 5 C 18734 2.51 5 N 5233 2.21 5 O 5727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 224": "NH1" <-> "NH2" Residue "2 ARG 319": "NH1" <-> "NH2" Residue "2 ARG 459": "NH1" <-> "NH2" Residue "2 ARG 489": "NH1" <-> "NH2" Residue "2 ARG 509": "NH1" <-> "NH2" Residue "2 ARG 534": "NH1" <-> "NH2" Residue "2 ARG 656": "NH1" <-> "NH2" Residue "2 ARG 705": "NH1" <-> "NH2" Residue "2 ARG 794": "NH1" <-> "NH2" Residue "2 ARG 808": "NH1" <-> "NH2" Residue "2 ARG 824": "NH1" <-> "NH2" Residue "2 ARG 854": "NH1" <-> "NH2" Residue "2 ARG 859": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 108": "NH1" <-> "NH2" Residue "3 ARG 208": "NH1" <-> "NH2" Residue "3 ARG 224": "NH1" <-> "NH2" Residue "3 ARG 291": "NH1" <-> "NH2" Residue "3 ARG 420": "NH1" <-> "NH2" Residue "3 ARG 435": "NH1" <-> "NH2" Residue "3 ARG 483": "NH1" <-> "NH2" Residue "3 ARG 657": "NH1" <-> "NH2" Residue "3 ARG 700": "NH1" <-> "NH2" Residue "3 ARG 734": "NH1" <-> "NH2" Residue "4 ARG 178": "NH1" <-> "NH2" Residue "4 ARG 234": "NH1" <-> "NH2" Residue "4 ARG 373": "NH1" <-> "NH2" Residue "4 ARG 388": "NH1" <-> "NH2" Residue "4 ARG 428": "NH1" <-> "NH2" Residue "4 ARG 499": "NH1" <-> "NH2" Residue "4 ARG 557": "NH1" <-> "NH2" Residue "4 ARG 559": "NH1" <-> "NH2" Residue "4 ARG 607": "NH1" <-> "NH2" Residue "4 ARG 681": "NH1" <-> "NH2" Residue "4 ARG 796": "NH1" <-> "NH2" Residue "4 ARG 827": "NH1" <-> "NH2" Residue "5 ARG 106": "NH1" <-> "NH2" Residue "5 ARG 407": "NH1" <-> "NH2" Residue "5 ARG 455": "NH1" <-> "NH2" Residue "5 ARG 460": "NH1" <-> "NH2" Residue "5 ARG 651": "NH1" <-> "NH2" Residue "6 ARG 112": "NH1" <-> "NH2" Residue "6 ARG 137": "NH1" <-> "NH2" Residue "6 ARG 176": "NH1" <-> "NH2" Residue "6 ARG 186": "NH1" <-> "NH2" Residue "6 ARG 190": "NH1" <-> "NH2" Residue "6 PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 275": "NH1" <-> "NH2" Residue "6 ARG 277": "NH1" <-> "NH2" Residue "6 ARG 280": "NH1" <-> "NH2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 375": "NH1" <-> "NH2" Residue "6 ARG 382": "NH1" <-> "NH2" Residue "6 ARG 424": "NH1" <-> "NH2" Residue "6 ARG 441": "NH1" <-> "NH2" Residue "6 ARG 446": "NH1" <-> "NH2" Residue "6 ARG 531": "NH1" <-> "NH2" Residue "6 ARG 691": "NH1" <-> "NH2" Residue "6 ARG 708": "NH1" <-> "NH2" Residue "6 ARG 781": "NH1" <-> "NH2" Residue "6 ARG 790": "NH1" <-> "NH2" Residue "7 ARG 152": "NH1" <-> "NH2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 ARG 214": "NH1" <-> "NH2" Residue "7 ARG 216": "NH1" <-> "NH2" Residue "7 TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 400": "NH1" <-> "NH2" Residue "7 ARG 451": "NH1" <-> "NH2" Residue "7 ARG 573": "NH1" <-> "NH2" Residue "7 ARG 577": "NH1" <-> "NH2" Residue "7 ARG 694": "NH1" <-> "NH2" Residue "7 ARG 703": "NH1" <-> "NH2" Residue "7 ARG 718": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29838 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 4714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4714 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 558} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "3" Number of atoms: 4745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4745 Classifications: {'peptide': 605} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 558} Chain breaks: 4 Chain: "4" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5081 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 17, 'PTRANS': 23, 'TRANS': 599} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 4962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4962 Classifications: {'peptide': 633} Link IDs: {'CIS': 18, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 587} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 4742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4742 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 29, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 564} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "7" Number of atoms: 5432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5432 Classifications: {'peptide': 689} Link IDs: {'CIS': 20, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 638} Chain breaks: 3 Chain: "2" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.39, per 1000 atoms: 0.52 Number of scatterers: 29838 At special positions: 0 Unit cell: (149.16, 138.6, 149.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 12 15.00 O 5727 8.00 N 5233 7.00 C 18734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS 5 183 " - pdb=" SG CYS 5 211 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 211 " distance=2.02 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 236 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 265 " - pdb=" SG CYS 7 289 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.97 Conformation dependent library (CDL) restraints added in 4.7 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7194 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 29 sheets defined 35.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.45 Creating SS restraints... Processing helix chain '2' and resid 202 through 216 removed outlier: 4.512A pdb=" N ALA 2 208 " --> pdb=" O ARG 2 205 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU 2 211 " --> pdb=" O ALA 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 226 through 236 removed outlier: 4.271A pdb=" N GLU 2 236 " --> pdb=" O ARG 2 232 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 252 Processing helix chain '2' and resid 254 through 261 Processing helix chain '2' and resid 264 through 282 removed outlier: 3.746A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 288 No H-bonds generated for 'chain '2' and resid 286 through 288' Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 412 through 414 No H-bonds generated for 'chain '2' and resid 412 through 414' Processing helix chain '2' and resid 478 through 486 removed outlier: 4.346A pdb=" N LYS 2 486 " --> pdb=" O ARG 2 482 " (cutoff:3.500A) Processing helix chain '2' and resid 491 through 501 removed outlier: 3.572A pdb=" N ILE 2 494 " --> pdb=" O ARG 2 491 " (cutoff:3.500A) Processing helix chain '2' and resid 509 through 520 removed outlier: 3.601A pdb=" N VAL 2 515 " --> pdb=" O ILE 2 511 " (cutoff:3.500A) Processing helix chain '2' and resid 549 through 559 removed outlier: 4.459A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS 2 554 " --> pdb=" O SER 2 550 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL 2 556 " --> pdb=" O ILE 2 552 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU 2 557 " --> pdb=" O LEU 2 553 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS 2 558 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 614 through 626 removed outlier: 4.038A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 675 Processing helix chain '2' and resid 689 through 704 removed outlier: 3.560A pdb=" N PHE 2 698 " --> pdb=" O ARG 2 694 " (cutoff:3.500A) Processing helix chain '2' and resid 760 through 773 removed outlier: 4.181A pdb=" N HIS 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) Processing helix chain '2' and resid 783 through 798 removed outlier: 5.094A pdb=" N ARG 2 795 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU 2 796 " --> pdb=" O LEU 2 793 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 823 removed outlier: 4.046A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 848 Processing helix chain '2' and resid 851 through 863 removed outlier: 3.673A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 855 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE 2 861 " --> pdb=" O ARG 2 858 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA 2 862 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 33 removed outlier: 3.678A pdb=" N PHE 3 28 " --> pdb=" O ARG 3 24 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN 3 29 " --> pdb=" O VAL 3 25 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU 3 30 " --> pdb=" O ARG 3 26 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE 3 31 " --> pdb=" O ARG 3 27 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU 3 32 " --> pdb=" O PHE 3 28 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 59 removed outlier: 4.318A pdb=" N ASP 3 40 " --> pdb=" O SER 3 37 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL 3 42 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN 3 51 " --> pdb=" O TYR 3 48 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR 3 56 " --> pdb=" O ALA 3 53 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN 3 57 " --> pdb=" O ALA 3 54 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP 3 58 " --> pdb=" O ASN 3 55 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP 3 59 " --> pdb=" O TYR 3 56 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 106 removed outlier: 3.930A pdb=" N ARG 3 104 " --> pdb=" O LEU 3 100 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU 3 105 " --> pdb=" O ASP 3 101 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 136 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 345 through 353 Processing helix chain '3' and resid 359 through 366 Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 415 through 426 removed outlier: 3.687A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG 3 420 " --> pdb=" O SER 3 416 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR 3 425 " --> pdb=" O PHE 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 461 through 464 No H-bonds generated for 'chain '3' and resid 461 through 464' Processing helix chain '3' and resid 480 through 490 removed outlier: 3.877A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) Processing helix chain '3' and resid 538 through 542 Processing helix chain '3' and resid 555 through 569 removed outlier: 4.115A pdb=" N HIS 3 564 " --> pdb=" O SER 3 560 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS 3 569 " --> pdb=" O VAL 3 565 " (cutoff:3.500A) Processing helix chain '3' and resid 653 through 665 removed outlier: 4.139A pdb=" N ARG 3 657 " --> pdb=" O ILE 3 653 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA 3 663 " --> pdb=" O TYR 3 659 " (cutoff:3.500A) Processing helix chain '3' and resid 676 through 693 removed outlier: 4.268A pdb=" N THR 3 692 " --> pdb=" O ASN 3 688 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 716 Processing helix chain '3' and resid 723 through 737 Processing helix chain '4' and resid 190 through 199 removed outlier: 3.975A pdb=" N PHE 4 197 " --> pdb=" O ASN 4 193 " (cutoff:3.500A) Processing helix chain '4' and resid 205 through 209 Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 255 through 263 removed outlier: 4.316A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 287 removed outlier: 3.977A pdb=" N ASP 4 286 " --> pdb=" O SER 4 282 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) Processing helix chain '4' and resid 295 through 298 No H-bonds generated for 'chain '4' and resid 295 through 298' Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 479 through 487 removed outlier: 5.935A pdb=" N GLU 4 484 " --> pdb=" O THR 4 480 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU 4 485 " --> pdb=" O ILE 4 481 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET 4 486 " --> pdb=" O GLU 4 482 " (cutoff:3.500A) Processing helix chain '4' and resid 503 through 514 removed outlier: 3.526A pdb=" N GLU 4 511 " --> pdb=" O ALA 4 507 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA 4 514 " --> pdb=" O ARG 4 510 " (cutoff:3.500A) Processing helix chain '4' and resid 516 through 526 removed outlier: 4.418A pdb=" N TYR 4 519 " --> pdb=" O GLU 4 516 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU 4 522 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE 4 526 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 544 Processing helix chain '4' and resid 574 through 584 removed outlier: 3.869A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 620 through 623 No H-bonds generated for 'chain '4' and resid 620 through 623' Processing helix chain '4' and resid 634 through 636 No H-bonds generated for 'chain '4' and resid 634 through 636' Processing helix chain '4' and resid 645 through 651 removed outlier: 4.030A pdb=" N GLU 4 650 " --> pdb=" O HIS 4 646 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 691 No H-bonds generated for 'chain '4' and resid 688 through 691' Processing helix chain '4' and resid 696 through 701 Processing helix chain '4' and resid 717 through 725 Processing helix chain '4' and resid 746 through 757 Processing helix chain '4' and resid 766 through 778 removed outlier: 3.530A pdb=" N TYR 4 774 " --> pdb=" O LEU 4 770 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 813 removed outlier: 3.645A pdb=" N SER 4 800 " --> pdb=" O GLN 4 797 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU 4 804 " --> pdb=" O MET 4 801 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA 4 805 " --> pdb=" O ILE 4 802 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 4 809 " --> pdb=" O GLU 4 806 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS 4 812 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU 4 813 " --> pdb=" O LYS 4 810 " (cutoff:3.500A) Processing helix chain '4' and resid 822 through 834 removed outlier: 4.397A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 36 Processing helix chain '5' and resid 45 through 55 removed outlier: 3.612A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 81 removed outlier: 3.888A pdb=" N LYS 5 77 " --> pdb=" O GLU 5 73 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 107 Proline residue: 5 88 - end of helix removed outlier: 3.941A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 153 through 155 No H-bonds generated for 'chain '5' and resid 153 through 155' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 362 removed outlier: 4.079A pdb=" N ARG 5 362 " --> pdb=" O LEU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 366 through 372 removed outlier: 3.574A pdb=" N ASN 5 372 " --> pdb=" O GLU 5 368 " (cutoff:3.500A) Processing helix chain '5' and resid 382 through 392 removed outlier: 4.103A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) Processing helix chain '5' and resid 422 through 432 removed outlier: 3.869A pdb=" N LYS 5 427 " --> pdb=" O SER 5 423 " (cutoff:3.500A) Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 487 through 499 removed outlier: 3.722A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN 5 499 " --> pdb=" O GLU 5 495 " (cutoff:3.500A) Processing helix chain '5' and resid 528 through 533 Processing helix chain '5' and resid 545 through 549 Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 580 through 591 Processing helix chain '5' and resid 597 through 609 removed outlier: 4.011A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) Processing helix chain '5' and resid 616 through 639 removed outlier: 4.635A pdb=" N GLU 5 639 " --> pdb=" O ILE 5 635 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 666 Processing helix chain '5' and resid 674 through 692 removed outlier: 4.068A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG 5 682 " --> pdb=" O ASP 5 678 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 120 Processing helix chain '6' and resid 136 through 146 removed outlier: 4.202A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 161 Processing helix chain '6' and resid 165 through 172 Processing helix chain '6' and resid 174 through 192 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 276 through 278 No H-bonds generated for 'chain '6' and resid 276 through 278' Processing helix chain '6' and resid 512 through 521 Processing helix chain '6' and resid 525 through 532 Processing helix chain '6' and resid 542 through 551 removed outlier: 3.976A pdb=" N GLN 6 550 " --> pdb=" O GLY 6 546 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET 6 551 " --> pdb=" O ILE 6 547 " (cutoff:3.500A) Processing helix chain '6' and resid 581 through 591 removed outlier: 3.971A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 643 No H-bonds generated for 'chain '6' and resid 641 through 643' Processing helix chain '6' and resid 647 through 657 removed outlier: 3.908A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 708 removed outlier: 3.669A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 735 Processing helix chain '6' and resid 750 through 758 Processing helix chain '6' and resid 768 through 782 removed outlier: 3.767A pdb=" N ARG 6 781 " --> pdb=" O LYS 6 778 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS 6 782 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 814 removed outlier: 3.547A pdb=" N ILE 6 804 " --> pdb=" O LEU 6 800 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG 6 805 " --> pdb=" O GLU 6 801 " (cutoff:3.500A) Processing helix chain '6' and resid 821 through 838 removed outlier: 4.190A pdb=" N VAL 6 838 " --> pdb=" O SER 6 834 " (cutoff:3.500A) Processing helix chain '7' and resid 14 through 24 removed outlier: 3.899A pdb=" N ASN 7 19 " --> pdb=" O ASN 7 15 " (cutoff:3.500A) Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 83 through 92 Processing helix chain '7' and resid 103 through 106 No H-bonds generated for 'chain '7' and resid 103 through 106' Processing helix chain '7' and resid 112 through 123 removed outlier: 3.622A pdb=" N ASN 7 123 " --> pdb=" O ARG 7 119 " (cutoff:3.500A) Processing helix chain '7' and resid 140 through 164 removed outlier: 3.956A pdb=" N LEU 7 154 " --> pdb=" O ASN 7 150 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER 7 163 " --> pdb=" O ASN 7 159 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU 7 164 " --> pdb=" O GLU 7 160 " (cutoff:3.500A) Processing helix chain '7' and resid 179 through 188 Processing helix chain '7' and resid 194 through 196 No H-bonds generated for 'chain '7' and resid 194 through 196' Processing helix chain '7' and resid 211 through 213 No H-bonds generated for 'chain '7' and resid 211 through 213' Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 364 through 366 No H-bonds generated for 'chain '7' and resid 364 through 366' Processing helix chain '7' and resid 398 through 406 removed outlier: 3.633A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 417 Processing helix chain '7' and resid 426 through 437 removed outlier: 4.094A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) Processing helix chain '7' and resid 467 through 476 removed outlier: 3.534A pdb=" N LYS 7 471 " --> pdb=" O GLN 7 468 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE 7 473 " --> pdb=" O LEU 7 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS 7 474 " --> pdb=" O LYS 7 471 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 493 No H-bonds generated for 'chain '7' and resid 490 through 493' Processing helix chain '7' and resid 532 through 542 removed outlier: 3.840A pdb=" N MET 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 588 through 591 No H-bonds generated for 'chain '7' and resid 588 through 591' Processing helix chain '7' and resid 606 through 621 removed outlier: 3.761A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 645 Processing helix chain '7' and resid 654 through 673 Processing helix chain '7' and resid 686 through 703 removed outlier: 3.730A pdb=" N LYS 7 701 " --> pdb=" O GLN 7 697 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU 7 702 " --> pdb=" O ALA 7 698 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 710 through 723 Processing helix chain '7' and resid 726 through 728 No H-bonds generated for 'chain '7' and resid 726 through 728' Processing sheet with id= A, first strand: chain '2' and resid 317 through 323 removed outlier: 3.557A pdb=" N THR 2 427 " --> pdb=" O SER 2 455 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 2 455 " --> pdb=" O THR 2 427 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA 2 453 " --> pdb=" O GLU 2 407 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE 2 409 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N SER 2 455 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LEU 2 411 " --> pdb=" O SER 2 455 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N LYS 2 457 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 679 through 682 Processing sheet with id= C, first strand: chain '2' and resid 629 through 631 Processing sheet with id= D, first strand: chain '3' and resid 180 through 185 removed outlier: 4.475A pdb=" N ARG 3 291 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 193 through 196 Processing sheet with id= F, first strand: chain '3' and resid 296 through 299 removed outlier: 3.570A pdb=" N LEU 3 320 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 545 through 549 Processing sheet with id= H, first strand: chain '3' and resid 495 through 497 Processing sheet with id= I, first strand: chain '4' and resid 325 through 327 Processing sheet with id= J, first strand: chain '4' and resid 397 through 400 Processing sheet with id= K, first strand: chain '4' and resid 439 through 442 Processing sheet with id= L, first strand: chain '4' and resid 704 through 708 removed outlier: 3.703A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL 4 589 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 654 through 656 Processing sheet with id= N, first strand: chain '4' and resid 339 through 344 removed outlier: 6.764A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 60 through 63 removed outlier: 6.692A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '5' and resid 333 through 335 removed outlier: 3.523A pdb=" N GLN 5 334 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '5' and resid 189 through 193 removed outlier: 6.962A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '5' and resid 296 through 301 Processing sheet with id= S, first strand: chain '5' and resid 436 through 440 removed outlier: 7.423A pdb=" N VAL 5 476 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR 5 439 " --> pdb=" O VAL 5 476 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N CYS 5 478 " --> pdb=" O THR 5 439 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER 5 518 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE 5 479 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU 5 520 " --> pdb=" O ILE 5 479 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain '5' and resid 501 through 503 Processing sheet with id= U, first strand: chain '6' and resid 151 through 154 removed outlier: 3.641A pdb=" N SER 6 266 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE 6 153 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain '6' and resid 458 through 460 removed outlier: 4.472A pdb=" N HIS 6 458 " --> pdb=" O THR 6 398 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR 6 398 " --> pdb=" O HIS 6 458 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP 6 393 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '6' and resid 570 through 574 removed outlier: 6.204A pdb=" N ILE 6 678 " --> pdb=" O ILE 6 571 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL 6 573 " --> pdb=" O ILE 6 678 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA 6 680 " --> pdb=" O VAL 6 573 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '6' and resid 660 through 664 Processing sheet with id= Y, first strand: chain '7' and resid 77 through 81 removed outlier: 6.252A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain '7' and resid 330 through 336 removed outlier: 3.719A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP 7 347 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '7' and resid 269 through 272 removed outlier: 6.838A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '7' and resid 596 through 599 removed outlier: 3.635A pdb=" N ILE 7 596 " --> pdb=" O ASN 7 455 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE 7 563 " --> pdb=" O VAL 7 456 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU 7 458 " --> pdb=" O ILE 7 563 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA 7 565 " --> pdb=" O LEU 7 458 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '7' and resid 496 through 498 924 hydrogen bonds defined for protein. 2445 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: 9.59 Time building geometry restraints manager: 11.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.55: 30019 1.55 - 1.90: 288 1.90 - 2.26: 0 2.26 - 2.61: 0 2.61 - 2.97: 1 Bond restraints: 30308 Sorted by residual: bond pdb=" C LYS 4 467 " pdb=" N VAL 4 469 " ideal model delta sigma weight residual 1.334 2.965 -1.631 1.26e-02 6.30e+03 1.68e+04 bond pdb=" N PRO 3 654 " pdb=" CD PRO 3 654 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" CA VAL 6 560 " pdb=" CB VAL 6 560 " ideal model delta sigma weight residual 1.540 1.593 -0.053 1.36e-02 5.41e+03 1.51e+01 bond pdb=" CA ILE 2 585 " pdb=" CB ILE 2 585 " ideal model delta sigma weight residual 1.540 1.591 -0.051 1.36e-02 5.41e+03 1.42e+01 bond pdb=" CA VAL 3 336 " pdb=" C VAL 3 336 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.27e-02 6.20e+03 1.06e+01 ... (remaining 30303 not shown) Histogram of bond angle deviations from ideal: 82.48 - 93.76: 3 93.76 - 105.03: 644 105.03 - 116.31: 20592 116.31 - 127.58: 19552 127.58 - 138.86: 219 Bond angle restraints: 41010 Sorted by residual: angle pdb=" CA LYS 4 467 " pdb=" C LYS 4 467 " pdb=" N VAL 4 469 " ideal model delta sigma weight residual 116.33 82.48 33.85 1.32e+00 5.74e-01 6.57e+02 angle pdb=" O LYS 4 467 " pdb=" C LYS 4 467 " pdb=" N VAL 4 469 " ideal model delta sigma weight residual 123.14 93.75 29.39 1.28e+00 6.10e-01 5.27e+02 angle pdb=" C LYS 4 467 " pdb=" N VAL 4 469 " pdb=" CA VAL 4 469 " ideal model delta sigma weight residual 120.56 91.40 29.16 1.28e+00 6.10e-01 5.19e+02 angle pdb=" C LEU 7 356 " pdb=" N PRO 7 357 " pdb=" CA PRO 7 357 " ideal model delta sigma weight residual 120.14 132.44 -12.30 1.06e+00 8.90e-01 1.35e+02 angle pdb=" N GLY 2 570 " pdb=" CA GLY 2 570 " pdb=" C GLY 2 570 " ideal model delta sigma weight residual 114.37 126.42 -12.05 1.26e+00 6.30e-01 9.15e+01 ... (remaining 41005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 18282 26.84 - 53.68: 340 53.68 - 80.52: 32 80.52 - 107.36: 6 107.36 - 134.20: 1 Dihedral angle restraints: 18661 sinusoidal: 7585 harmonic: 11076 Sorted by residual: dihedral pdb=" CA GLY 6 600 " pdb=" C GLY 6 600 " pdb=" N LYS 6 601 " pdb=" CA LYS 6 601 " ideal model delta harmonic sigma weight residual 180.00 45.80 134.20 0 5.00e+00 4.00e-02 7.20e+02 dihedral pdb=" CB CYS 5 186 " pdb=" SG CYS 5 186 " pdb=" SG CYS 5 211 " pdb=" CB CYS 5 211 " ideal model delta sinusoidal sigma weight residual 93.00 178.88 -85.88 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CA THR 3 172 " pdb=" C THR 3 172 " pdb=" N ALA 3 173 " pdb=" CA ALA 3 173 " ideal model delta harmonic sigma weight residual 0.00 -44.36 44.36 0 5.00e+00 4.00e-02 7.87e+01 ... (remaining 18658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3972 0.079 - 0.157: 722 0.157 - 0.236: 69 0.236 - 0.314: 6 0.314 - 0.393: 1 Chirality restraints: 4770 Sorted by residual: chirality pdb=" CA GLN 7 209 " pdb=" N GLN 7 209 " pdb=" C GLN 7 209 " pdb=" CB GLN 7 209 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA ASN 2 366 " pdb=" N ASN 2 366 " pdb=" C ASN 2 366 " pdb=" CB ASN 2 366 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA LYS 7 486 " pdb=" N LYS 7 486 " pdb=" C LYS 7 486 " pdb=" CB LYS 7 486 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4767 not shown) Planarity restraints: 5273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS 4 467 " -0.182 2.00e-02 2.50e+03 2.72e-01 7.39e+02 pdb=" C LYS 4 467 " 0.445 2.00e-02 2.50e+03 pdb=" O LYS 4 467 " -0.253 2.00e-02 2.50e+03 pdb=" N VAL 4 469 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 653 " -0.126 5.00e-02 4.00e+02 1.77e-01 5.00e+01 pdb=" N PRO 3 654 " 0.305 5.00e-02 4.00e+02 pdb=" CA PRO 3 654 " -0.098 5.00e-02 4.00e+02 pdb=" CD PRO 3 654 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 5 18 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO 5 19 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO 5 19 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO 5 19 " -0.038 5.00e-02 4.00e+02 ... (remaining 5270 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 227 2.38 - 3.01: 19695 3.01 - 3.64: 44617 3.64 - 4.27: 65054 4.27 - 4.90: 105317 Nonbonded interactions: 234910 Sorted by model distance: nonbonded pdb=" OD2 ASP 7 453 " pdb=" OG SER 7 562 " model vdw 1.749 2.440 nonbonded pdb=" OD2 ASP 6 355 " pdb=" N GLY 6 383 " model vdw 1.802 2.520 nonbonded pdb=" NH1 ARG 2 327 " pdb=" OE2 GLU 5 269 " model vdw 1.851 2.520 nonbonded pdb=" O SER 2 298 " pdb=" NH2 ARG 2 319 " model vdw 1.872 2.520 nonbonded pdb=" NZ LYS 5 442 " pdb=" O LYS 5 484 " model vdw 1.919 2.520 ... (remaining 234905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.130 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 75.550 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.014 1.631 30308 Z= 0.715 Angle : 1.572 33.847 41010 Z= 1.029 Chirality : 0.060 0.393 4770 Planarity : 0.007 0.272 5273 Dihedral : 10.982 134.195 11452 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 29.23 Ramachandran Plot: Outliers : 1.12 % Allowed : 7.87 % Favored : 91.00 % Rotamer: Outliers : 0.37 % Allowed : 2.47 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 3.21 % Twisted Proline : 0.67 % Twisted General : 0.50 % 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: -4.26 (0.10), residues: 3734 helix: -3.37 (0.09), residues: 1282 sheet: -2.01 (0.18), residues: 559 loop : -2.65 (0.11), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP 2 589 HIS 0.016 0.002 HIS 4 465 PHE 0.037 0.003 PHE 6 454 TYR 0.038 0.003 TYR 3 211 ARG 0.009 0.001 ARG 7 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 962 time to evaluate : 3.438 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: 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: symmetry clash outliers start: 12 outliers final: 1 residues processed: 968 average time/residue: 0.4796 time to fit residues: 694.5891 Evaluate side-chains 621 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 620 time to evaluate : 3.544 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2749 time to fit residues: 5.1839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.7980 chunk 284 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 341 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 333 GLN 2 391 GLN 2 658 ASN 2 779 HIS 2 849 GLN 2 856 GLN 3 330 HIS 3 349 ASN ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 374 HIS 3 492 GLN 3 554 ASN 3 569 HIS ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 688 ASN ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 253 GLN 4 263 ASN 4 318 ASN 4 350 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 400 GLN 4 465 HIS 4 646 HIS 4 757 HIS 5 49 GLN 5 67 HIS 5 155 HIS 5 334 GLN 5 359 GLN ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 424 GLN 5 494 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 632 GLN ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 570 ASN ** 6 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 658 GLN 6 690 ASN 6 698 ASN ** 6 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 144 ASN 7 271 GLN ** 7 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 334 HIS 7 538 HIS 7 544 GLN ** 7 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30308 Z= 0.276 Angle : 1.002 16.270 41010 Z= 0.513 Chirality : 0.050 0.308 4770 Planarity : 0.005 0.063 5273 Dihedral : 7.884 71.549 4201 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.94 % Allowed : 7.28 % Favored : 91.78 % Rotamer: Outliers : 3.57 % Allowed : 12.18 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 3.29 % Twisted Proline : 0.67 % Twisted General : 0.44 % 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: -2.85 (0.12), residues: 3736 helix: -1.47 (0.13), residues: 1274 sheet: -1.65 (0.19), residues: 592 loop : -2.25 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP 2 589 HIS 0.011 0.001 HIS 4 465 PHE 0.047 0.002 PHE 2 484 TYR 0.021 0.002 TYR 5 301 ARG 0.008 0.001 ARG 5 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 742 time to evaluate : 3.395 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 50 residues processed: 806 average time/residue: 0.4514 time to fit residues: 572.1865 Evaluate side-chains 658 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 608 time to evaluate : 3.389 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.3012 time to fit residues: 32.5477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 0.1980 chunk 105 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 232 optimal weight: 0.0870 chunk 94 optimal weight: 0.8980 chunk 342 optimal weight: 3.9990 chunk 369 optimal weight: 0.9980 chunk 304 optimal weight: 0.9990 chunk 339 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 294 HIS 2 569 GLN 3 351 ASN ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 581 ASN ** 5 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 583 GLN 6 673 ASN 6 833 GLN ** 7 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS ** 7 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 662 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30308 Z= 0.223 Angle : 0.923 16.200 41010 Z= 0.467 Chirality : 0.048 0.296 4770 Planarity : 0.005 0.059 5273 Dihedral : 7.271 68.816 4201 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.08 % Favored : 90.95 % Rotamer: Outliers : 2.75 % Allowed : 15.42 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.38 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.20 (0.13), residues: 3736 helix: -0.63 (0.14), residues: 1288 sheet: -1.41 (0.20), residues: 543 loop : -2.08 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 476 HIS 0.008 0.001 HIS 3 503 PHE 0.038 0.002 PHE 2 484 TYR 0.033 0.002 TYR 6 621 ARG 0.006 0.001 ARG 4 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 663 time to evaluate : 3.122 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 34 residues processed: 733 average time/residue: 0.4209 time to fit residues: 488.7992 Evaluate side-chains 618 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 584 time to evaluate : 3.531 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2819 time to fit residues: 22.4426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 229 optimal weight: 0.5980 chunk 343 optimal weight: 4.9990 chunk 363 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 325 optimal weight: 6.9990 chunk 97 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 184 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 140 ASN ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 632 GLN ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 357 GLN ** 7 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS 7 554 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30308 Z= 0.247 Angle : 0.898 15.836 41010 Z= 0.451 Chirality : 0.047 0.289 4770 Planarity : 0.004 0.055 5273 Dihedral : 6.993 66.332 4201 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.81 % Favored : 90.23 % Rotamer: Outliers : 3.05 % Allowed : 17.64 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.38 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.99 (0.13), residues: 3736 helix: -0.33 (0.14), residues: 1287 sheet: -1.32 (0.21), residues: 558 loop : -2.05 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 2 589 HIS 0.006 0.001 HIS 6 735 PHE 0.039 0.002 PHE 3 421 TYR 0.024 0.002 TYR 6 621 ARG 0.006 0.000 ARG 4 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 643 time to evaluate : 3.459 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 outliers start: 100 outliers final: 53 residues processed: 694 average time/residue: 0.4238 time to fit residues: 469.5478 Evaluate side-chains 629 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 576 time to evaluate : 3.764 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.2932 time to fit residues: 33.4432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 1.9990 chunk 206 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 326 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 263 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30308 Z= 0.257 Angle : 0.888 15.738 41010 Z= 0.448 Chirality : 0.047 0.289 4770 Planarity : 0.005 0.063 5273 Dihedral : 6.874 66.250 4201 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 1.02 % Allowed : 8.83 % Favored : 90.15 % Rotamer: Outliers : 2.32 % Allowed : 19.51 % Favored : 78.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.35 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.89 (0.13), residues: 3736 helix: -0.18 (0.14), residues: 1288 sheet: -1.26 (0.21), residues: 552 loop : -2.04 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 356 HIS 0.005 0.001 HIS 4 413 PHE 0.034 0.002 PHE 3 421 TYR 0.022 0.002 TYR 6 621 ARG 0.006 0.000 ARG 7 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 622 time to evaluate : 3.774 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 outliers start: 76 outliers final: 28 residues processed: 676 average time/residue: 0.4176 time to fit residues: 449.3016 Evaluate side-chains 586 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 558 time to evaluate : 3.491 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2964 time to fit residues: 20.0457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 0.5980 chunk 327 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 363 optimal weight: 0.5980 chunk 301 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 263 ASN 4 287 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN ** 7 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30308 Z= 0.230 Angle : 0.888 15.656 41010 Z= 0.442 Chirality : 0.047 0.285 4770 Planarity : 0.004 0.062 5273 Dihedral : 6.721 65.535 4201 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.70 % Favored : 90.26 % Rotamer: Outliers : 1.95 % Allowed : 21.40 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 3.38 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.80 (0.13), residues: 3736 helix: -0.08 (0.14), residues: 1302 sheet: -1.22 (0.22), residues: 529 loop : -2.01 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 356 HIS 0.008 0.001 HIS 4 259 PHE 0.032 0.002 PHE 3 735 TYR 0.029 0.002 TYR 6 621 ARG 0.014 0.000 ARG 4 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 590 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 131, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 99, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 209, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 196, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable