Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 23:13:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwb_34308/10_2023/8gwb_34308.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwb_34308/10_2023/8gwb_34308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwb_34308/10_2023/8gwb_34308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwb_34308/10_2023/8gwb_34308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwb_34308/10_2023/8gwb_34308.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwb_34308/10_2023/8gwb_34308.pdb" } resolution = 2.75 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= -0.000 sd= 0.053 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 8 6.06 5 P 54 5.49 5 S 157 5.16 5 C 13689 2.51 5 N 3681 2.21 5 O 4288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A GLU 919": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F GLU 447": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "G GLU 3": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 21879 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna3p': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 88.954 57.320 63.002 1.00 31.45 S ATOM 2487 SG CYS A 306 89.585 59.411 60.028 1.00 42.65 S ATOM 2519 SG CYS A 310 87.261 56.343 60.075 1.00 52.03 S ATOM 3927 SG CYS A 487 90.091 69.817 80.117 1.00 35.69 S ATOM 5180 SG CYS A 645 91.497 71.748 77.082 1.00 53.57 S ATOM 5186 SG CYS A 646 91.811 67.874 77.373 1.00 53.06 S ATOM 12035 SG CYS F 16 60.647 69.650 134.275 1.00180.59 S ATOM 12050 SG CYS F 19 58.927 66.440 135.640 1.00182.13 S ATOM 11953 SG CYS F 5 49.538 76.179 131.797 1.00182.59 S ATOM 11974 SG CYS F 8 49.445 78.126 135.000 1.00190.86 S ATOM 12112 SG CYS F 26 51.642 79.419 132.284 1.00188.57 S ATOM 12129 SG CYS F 29 52.777 76.427 134.031 1.00193.40 S ATOM 12294 SG CYS F 50 76.363 76.882 122.167 1.00163.85 S ATOM 12324 SG CYS F 55 78.347 74.790 124.518 1.00172.84 S ATOM 12457 SG CYS F 72 77.087 77.874 125.773 1.00160.49 S ATOM 16548 SG CYS E 16 105.825 65.355 121.422 1.00161.69 S ATOM 16563 SG CYS E 19 105.603 61.610 122.172 1.00168.49 S ATOM 16466 SG CYS E 5 94.156 63.654 128.424 1.00189.90 S ATOM 16487 SG CYS E 8 94.606 65.241 131.846 1.00200.92 S ATOM 16625 SG CYS E 26 93.566 67.468 129.032 1.00189.25 S ATOM 16642 SG CYS E 29 97.161 66.024 129.368 1.00195.34 S ATOM 16807 SG CYS E 50 105.717 81.183 109.224 1.00167.63 S ATOM 16837 SG CYS E 55 109.424 80.949 108.484 1.00154.77 S ATOM 16970 SG CYS E 72 108.277 83.165 111.358 1.00188.61 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.59 residue: pdb=" N AMET E 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.59 Time building chain proxies: 15.60, per 1000 atoms: 0.71 Number of scatterers: 21879 At special positions: 0 Unit cell: (151.7, 141.04, 180.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 Mn 2 24.99 S 157 16.00 P 54 15.00 O 4288 8.00 N 3681 7.00 C 13689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 9.12 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " Number of angles added : 27 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 35 sheets defined 39.6% alpha, 13.0% beta 20 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 8.15 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.935A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.638A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.636A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.144A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.526A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Proline residue: A 243 - end of helix removed outlier: 4.255A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.520A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.509A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.523A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.942A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.399A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.216A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.724A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.807A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.594A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.559A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.685A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 856 through 865 Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 874 through 902 removed outlier: 4.010A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 removed outlier: 4.454A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.809A pdb=" N THR A 926 " --> pdb=" O ALA A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.159A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 95 removed outlier: 3.653A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.526A pdb=" N ASN B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.142A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.693A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 48 removed outlier: 4.007A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 80 removed outlier: 4.074A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.969A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.754A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.905A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 103 through 111 removed outlier: 3.571A pdb=" N THR F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 removed outlier: 3.644A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 147 removed outlier: 3.663A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 273 removed outlier: 4.164A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.733A pdb=" N ALA F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 325 removed outlier: 4.758A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 4.318A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 423 removed outlier: 3.764A pdb=" N PHE F 422 " --> pdb=" O PRO F 419 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 Processing helix chain 'F' and resid 445 through 454 removed outlier: 3.555A pdb=" N ASP F 450 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 503 Processing helix chain 'F' and resid 504 through 507 removed outlier: 3.637A pdb=" N ARG F 507 " --> pdb=" O PRO F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 504 through 507' Processing helix chain 'F' and resid 515 through 523 removed outlier: 4.144A pdb=" N ASN F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 566 removed outlier: 3.600A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.919A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 125 removed outlier: 4.207A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 265 through 273 Processing helix chain 'E' and resid 287 through 299 removed outlier: 4.528A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 removed outlier: 4.831A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 390 removed outlier: 3.581A pdb=" N LEU E 384 " --> pdb=" O THR E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 429 removed outlier: 3.537A pdb=" N ARG E 427 " --> pdb=" O ASN E 423 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 428 " --> pdb=" O SER E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 3.634A pdb=" N VAL E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 501 removed outlier: 3.763A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 497 " --> pdb=" O ILE E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 removed outlier: 7.008A pdb=" N ALA E 505 " --> pdb=" O ARG E 502 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG E 507 " --> pdb=" O PRO E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 524 removed outlier: 3.946A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.789A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 102 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.893A pdb=" N VAL A 42 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.074A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.548A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.548A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560 removed outlier: 7.051A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 757 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 129 removed outlier: 3.556A pdb=" N ALA D 188 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 160 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 129 removed outlier: 3.556A pdb=" N ALA D 188 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 160 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'F' and resid 24 through 25 removed outlier: 4.210A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.619A pdb=" N ALA F 85 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 163 through 166 removed outlier: 7.170A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 182 through 187 removed outlier: 6.711A pdb=" N PHE F 182 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU F 197 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY F 184 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE F 195 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 200 through 201 Processing sheet with id=AC2, first strand: chain 'F' and resid 330 through 332 removed outlier: 5.913A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 544 through 545 removed outlier: 6.937A pdb=" N VAL F 544 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ILE F 575 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE F 472 " --> pdb=" O CYS F 574 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N MET F 576 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N AMET F 474 " --> pdb=" O MET F 576 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LYS F 473 " --> pdb=" O LEU F 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 481 through 482 removed outlier: 4.050A pdb=" N THR F 481 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE F 488 " --> pdb=" O THR F 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 511 through 512 removed outlier: 6.130A pdb=" N PHE F 511 " --> pdb=" O GLN F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC7, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC8, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AC9, first strand: chain 'E' and resid 153 through 159 removed outlier: 3.713A pdb=" N ARG E 155 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL E 157 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N GLU E 162 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AD2, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AD3, first strand: chain 'E' and resid 330 through 332 removed outlier: 6.526A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS E 358 " --> pdb=" O TYR E 306 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY E 400 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU E 280 " --> pdb=" O GLY E 400 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 366 through 367 removed outlier: 7.094A pdb=" N THR E 366 " --> pdb=" O ARG E 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AD6, first strand: chain 'E' and resid 530 through 532 removed outlier: 6.121A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.272A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR G 35 " --> pdb=" O GLY G 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.576A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2157 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 9.21 Time building geometry restraints manager: 9.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.23: 508 1.23 - 1.56: 21606 1.56 - 1.89: 331 1.89 - 2.22: 0 2.22 - 2.55: 1 Bond restraints: 22446 Sorted by residual: bond pdb=" CB PRO E 284 " pdb=" CG PRO E 284 " ideal model delta sigma weight residual 1.492 2.547 -1.055 5.00e-02 4.00e+02 4.45e+02 bond pdb=" CG PRO E 284 " pdb=" CD PRO E 284 " ideal model delta sigma weight residual 1.503 0.904 0.599 3.40e-02 8.65e+02 3.11e+02 bond pdb=" C ASN A 52 " pdb=" N CYS A 53 " ideal model delta sigma weight residual 1.333 1.092 0.240 1.38e-02 5.25e+03 3.03e+02 bond pdb=" C THR A 51 " pdb=" N ASN A 52 " ideal model delta sigma weight residual 1.330 1.135 0.195 1.36e-02 5.41e+03 2.05e+02 bond pdb=" N PRO E 284 " pdb=" CD PRO E 284 " ideal model delta sigma weight residual 1.473 1.556 -0.083 1.40e-02 5.10e+03 3.55e+01 ... (remaining 22441 not shown) Histogram of bond angle deviations from ideal: 10.10 - 36.79: 1 36.79 - 63.48: 0 63.48 - 90.18: 2 90.18 - 116.87: 15981 116.87 - 143.57: 14785 Bond angle restraints: 30769 Sorted by residual: angle pdb=" CB PRO E 284 " pdb=" CG PRO E 284 " pdb=" CD PRO E 284 " ideal model delta sigma weight residual 106.10 10.10 96.00 3.20e+00 9.77e-02 9.00e+02 angle pdb=" O ASN A 52 " pdb=" C ASN A 52 " pdb=" N CYS A 53 " ideal model delta sigma weight residual 121.83 96.89 24.94 1.33e+00 5.65e-01 3.52e+02 angle pdb=" N PRO E 284 " pdb=" CA PRO E 284 " pdb=" CB PRO E 284 " ideal model delta sigma weight residual 103.25 88.58 14.67 1.05e+00 9.07e-01 1.95e+02 angle pdb=" CA ASN A 52 " pdb=" C ASN A 52 " pdb=" N CYS A 53 " ideal model delta sigma weight residual 116.19 135.61 -19.42 1.66e+00 3.63e-01 1.37e+02 angle pdb=" CA PRO E 284 " pdb=" N PRO E 284 " pdb=" CD PRO E 284 " ideal model delta sigma weight residual 112.00 96.57 15.43 1.40e+00 5.10e-01 1.21e+02 ... (remaining 30764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.85: 12384 25.85 - 51.70: 853 51.70 - 77.56: 69 77.56 - 103.41: 10 103.41 - 129.26: 2 Dihedral angle restraints: 13318 sinusoidal: 5462 harmonic: 7856 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 142.48 37.52 0 5.00e+00 4.00e-02 5.63e+01 dihedral pdb=" C5' U M 2 " pdb=" C4' U M 2 " pdb=" C3' U M 2 " pdb=" O3' U M 2 " ideal model delta sinusoidal sigma weight residual 147.00 96.10 50.90 1 8.00e+00 1.56e-02 5.54e+01 dihedral pdb=" O4' U M 2 " pdb=" C4' U M 2 " pdb=" C3' U M 2 " pdb=" C2' U M 2 " ideal model delta sinusoidal sigma weight residual 24.00 -26.74 50.74 1 8.00e+00 1.56e-02 5.51e+01 ... (remaining 13315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3430 0.100 - 0.201: 134 0.201 - 0.301: 4 0.301 - 0.402: 2 0.402 - 0.502: 1 Chirality restraints: 3571 Sorted by residual: chirality pdb=" P A M 1 " pdb=" OP1 A M 1 " pdb=" OP2 A M 1 " pdb=" O5' A M 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" C3' A M 1 " pdb=" C4' A M 1 " pdb=" O3' A M 1 " pdb=" C2' A M 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA PRO E 284 " pdb=" N PRO E 284 " pdb=" C PRO E 284 " pdb=" CB PRO E 284 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 3568 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 52 " 0.046 2.00e-02 2.50e+03 7.97e-02 6.36e+01 pdb=" C ASN A 52 " -0.138 2.00e-02 2.50e+03 pdb=" O ASN A 52 " 0.038 2.00e-02 2.50e+03 pdb=" N CYS A 53 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 1 " 0.026 2.00e-02 2.50e+03 6.25e-02 3.91e+01 pdb=" C ASN G 1 " -0.108 2.00e-02 2.50e+03 pdb=" O ASN G 1 " 0.045 2.00e-02 2.50e+03 pdb=" N ASN G 2 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " -0.092 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO B 183 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " -0.074 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 20 2.23 - 2.89: 8875 2.89 - 3.56: 31700 3.56 - 4.23: 52281 4.23 - 4.90: 85658 Nonbonded interactions: 178534 Sorted by model distance: nonbonded pdb=" N ASN G 1 " pdb=" P A M 1 " model vdw 1.556 3.480 nonbonded pdb="MN MN A1003 " pdb=" O HOH M 102 " model vdw 2.106 2.320 nonbonded pdb="MN MN A1004 " pdb=" O HOH A1103 " model vdw 2.134 2.320 nonbonded pdb=" N2 G I 11 " pdb=" O2 C J 49 " model vdw 2.135 2.496 nonbonded pdb=" O PHE F 145 " pdb=" OG SER F 148 " model vdw 2.141 2.440 ... (remaining 178529 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 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) } 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 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: 20.060 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 77.860 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0099 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 : 0.009 1.055 22446 Z= 0.480 Angle : 1.065 96.004 30769 Z= 0.565 Chirality : 0.046 0.502 3571 Planarity : 0.007 0.142 3732 Dihedral : 16.016 129.259 8250 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.52 % Favored : 92.29 % Rotamer: Outliers : 2.25 % Allowed : 24.39 % Favored : 73.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -2.40 (0.15), residues: 2639 helix: -0.53 (0.17), residues: 946 sheet: -2.16 (0.34), residues: 199 loop : -2.30 (0.15), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 241 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 5 residues processed: 285 average time/residue: 1.0827 time to fit residues: 364.5662 Evaluate side-chains 149 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 2.489 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 2 average time/residue: 0.2901 time to fit residues: 4.2187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 898 HIS ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN F 9 ASN ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0694 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 22446 Z= 0.241 Angle : 0.727 12.756 30769 Z= 0.374 Chirality : 0.044 0.214 3571 Planarity : 0.006 0.107 3732 Dihedral : 6.973 126.908 3533 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.90 % Favored : 91.99 % Rotamer: Outliers : 4.76 % Allowed : 23.03 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -2.20 (0.15), residues: 2639 helix: -0.46 (0.16), residues: 955 sheet: -1.58 (0.31), residues: 239 loop : -2.20 (0.15), residues: 1445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 169 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 24 residues processed: 249 average time/residue: 1.1621 time to fit residues: 339.2540 Evaluate side-chains 162 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 2.331 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.4950 time to fit residues: 8.1784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 194 optimal weight: 0.0060 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS A 650 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 245 HIS ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1413 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 22446 Z= 0.358 Angle : 0.895 15.968 30769 Z= 0.463 Chirality : 0.051 0.296 3571 Planarity : 0.007 0.103 3732 Dihedral : 7.963 124.749 3533 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.27 % Favored : 90.62 % Rotamer: Outliers : 5.87 % Allowed : 22.98 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -2.71 (0.15), residues: 2639 helix: -1.08 (0.16), residues: 935 sheet: -1.74 (0.32), residues: 207 loop : -2.36 (0.15), residues: 1497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 170 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 42 residues processed: 279 average time/residue: 1.0220 time to fit residues: 339.2658 Evaluate side-chains 186 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 37 residues processed: 5 average time/residue: 0.6100 time to fit residues: 6.9647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 162 optimal weight: 0.0000 chunk 242 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 126 optimal weight: 0.0770 chunk 230 optimal weight: 0.0270 chunk 69 optimal weight: 0.6980 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN A 215 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN A 752 HIS ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 489 ASN F 492 GLN F 518 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1111 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22446 Z= 0.174 Angle : 0.645 9.577 30769 Z= 0.326 Chirality : 0.042 0.186 3571 Planarity : 0.005 0.085 3732 Dihedral : 6.950 124.220 3533 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.72 % Favored : 93.20 % Rotamer: Outliers : 4.23 % Allowed : 25.76 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -2.06 (0.15), residues: 2639 helix: -0.44 (0.16), residues: 931 sheet: -1.36 (0.33), residues: 208 loop : -2.05 (0.15), residues: 1500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 154 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 41 residues processed: 230 average time/residue: 1.1100 time to fit residues: 303.1645 Evaluate side-chains 183 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 2.377 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 34 residues processed: 8 average time/residue: 0.9954 time to fit residues: 12.8968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 219 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 ASN F 492 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1439 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22446 Z= 0.242 Angle : 0.739 13.740 30769 Z= 0.373 Chirality : 0.045 0.231 3571 Planarity : 0.006 0.074 3732 Dihedral : 7.276 125.126 3533 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.12 % Favored : 90.81 % Rotamer: Outliers : 4.50 % Allowed : 26.20 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -2.10 (0.15), residues: 2639 helix: -0.49 (0.16), residues: 906 sheet: -1.11 (0.34), residues: 212 loop : -2.09 (0.15), residues: 1521 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 144 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 46 residues processed: 220 average time/residue: 1.0877 time to fit residues: 284.9200 Evaluate side-chains 184 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 2.260 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 38 residues processed: 9 average time/residue: 0.6500 time to fit residues: 10.8348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 257 optimal weight: 0.0980 chunk 213 optimal weight: 0.1980 chunk 119 optimal weight: 40.0000 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN D 118 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1473 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22446 Z= 0.223 Angle : 0.703 12.741 30769 Z= 0.353 Chirality : 0.044 0.209 3571 Planarity : 0.005 0.068 3732 Dihedral : 7.250 124.789 3533 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.36 % Favored : 91.57 % Rotamer: Outliers : 4.28 % Allowed : 27.13 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -2.05 (0.16), residues: 2639 helix: -0.45 (0.16), residues: 917 sheet: -1.12 (0.34), residues: 211 loop : -2.04 (0.15), residues: 1511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 147 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 50 residues processed: 222 average time/residue: 1.0520 time to fit residues: 280.5350 Evaluate side-chains 190 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 140 time to evaluate : 2.309 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 42 residues processed: 9 average time/residue: 0.6700 time to fit residues: 11.1372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 146 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 160 optimal weight: 0.0570 chunk 156 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN D 118 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 503 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1521 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22446 Z= 0.208 Angle : 0.688 13.319 30769 Z= 0.347 Chirality : 0.043 0.190 3571 Planarity : 0.005 0.059 3732 Dihedral : 7.211 125.374 3533 Min Nonbonded Distance : 1.475 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.58 % Favored : 91.34 % Rotamer: Outliers : 4.01 % Allowed : 27.17 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -2.02 (0.16), residues: 2639 helix: -0.40 (0.17), residues: 922 sheet: -1.10 (0.32), residues: 248 loop : -2.06 (0.16), residues: 1469 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 148 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 56 residues processed: 221 average time/residue: 1.0284 time to fit residues: 271.9390 Evaluate side-chains 196 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 140 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 48 residues processed: 9 average time/residue: 0.4715 time to fit residues: 9.2413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 162 optimal weight: 0.0670 chunk 174 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 ASN F 388 ASN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1483 moved from start: 0.7221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22446 Z= 0.184 Angle : 0.683 15.239 30769 Z= 0.337 Chirality : 0.043 0.296 3571 Planarity : 0.005 0.060 3732 Dihedral : 7.057 125.549 3533 Min Nonbonded Distance : 1.535 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.44 % Rotamer: Outliers : 3.44 % Allowed : 28.19 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.90 (0.16), residues: 2639 helix: -0.19 (0.17), residues: 913 sheet: -1.08 (0.32), residues: 257 loop : -2.06 (0.16), residues: 1469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 142 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 55 residues processed: 208 average time/residue: 1.0597 time to fit residues: 264.1792 Evaluate side-chains 193 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 138 time to evaluate : 2.461 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 51 residues processed: 5 average time/residue: 0.6018 time to fit residues: 7.3561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 238 optimal weight: 3.9990 chunk 143 optimal weight: 0.0070 chunk 104 optimal weight: 0.1980 chunk 187 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 156 optimal weight: 0.1980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1388 moved from start: 0.7318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22446 Z= 0.165 Angle : 0.650 13.434 30769 Z= 0.321 Chirality : 0.041 0.240 3571 Planarity : 0.005 0.061 3732 Dihedral : 6.777 126.071 3533 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.37 % Favored : 92.56 % Rotamer: Outliers : 3.26 % Allowed : 28.41 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.71 (0.16), residues: 2639 helix: -0.02 (0.17), residues: 922 sheet: -0.86 (0.31), residues: 267 loop : -2.00 (0.16), residues: 1450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 141 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 56 residues processed: 203 average time/residue: 1.0870 time to fit residues: 263.0376 Evaluate side-chains 189 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 133 time to evaluate : 2.587 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 54 residues processed: 4 average time/residue: 1.2563 time to fit residues: 9.4412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 2.9990 chunk 154 optimal weight: 0.0170 chunk 119 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 167 optimal weight: 0.5980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 118 ASN ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1491 moved from start: 0.7617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22446 Z= 0.184 Angle : 0.674 13.328 30769 Z= 0.332 Chirality : 0.043 0.339 3571 Planarity : 0.005 0.060 3732 Dihedral : 6.838 126.320 3533 Min Nonbonded Distance : 1.464 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.13 % Favored : 91.80 % Rotamer: Outliers : 2.87 % Allowed : 29.16 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.70 (0.16), residues: 2639 helix: -0.06 (0.17), residues: 928 sheet: -0.85 (0.32), residues: 257 loop : -1.96 (0.16), residues: 1454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 137 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 50 residues processed: 193 average time/residue: 1.0632 time to fit residues: 246.8163 Evaluate side-chains 188 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 138 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 49 residues processed: 3 average time/residue: 0.3706 time to fit residues: 5.0355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 194 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 0.0040 chunk 211 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 217 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 overall best weight: 0.5270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.265445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.250331 restraints weight = 81776.492| |-----------------------------------------------------------------------------| r_work (start): 0.5123 rms_B_bonded: 3.00 r_work: 0.4953 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4938 r_free = 0.4938 target_work(ls_wunit_k1) = 0.227 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4938 r_free = 0.4938 target_work(ls_wunit_k1) = 0.227 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.4938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1451 moved from start: 0.7685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22446 Z= 0.164 Angle : 0.651 12.400 30769 Z= 0.321 Chirality : 0.042 0.281 3571 Planarity : 0.005 0.115 3732 Dihedral : 6.688 126.268 3533 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.22 % Favored : 92.71 % Rotamer: Outliers : 2.47 % Allowed : 29.73 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.58 (0.16), residues: 2639 helix: 0.10 (0.17), residues: 916 sheet: -0.73 (0.32), residues: 268 loop : -1.93 (0.16), residues: 1455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6840.85 seconds wall clock time: 124 minutes 0.31 seconds (7440.31 seconds total)