Starting phenix.real_space_refine (version: dev) on Sun Dec 18 14:54:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/12_2022/7lla_23413_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/12_2022/7lla_23413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/12_2022/7lla_23413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/12_2022/7lla_23413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/12_2022/7lla_23413_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/12_2022/7lla_23413_updated_updated.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B GLU 718": "OE1" <-> "OE2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B GLU 891": "OE1" <-> "OE2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 507": "NH1" <-> "NH2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 718": "OE1" <-> "OE2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C GLU 792": "OE1" <-> "OE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 891": "OE1" <-> "OE2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D GLU 718": "OE1" <-> "OE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D GLU 792": "OE1" <-> "OE2" Residue "D GLU 795": "OE1" <-> "OE2" Residue "D GLU 891": "OE1" <-> "OE2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D ARG 995": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 31900 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Unusual residues: {'ACO': 1, 'OAA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACO': 1, 'OAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 31.59, per 1000 atoms: 0.99 Number of scatterers: 31900 At special positions: 0 Unit cell: (162.69, 140.07, 171.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 12 15.00 O 5940 8.00 N 5388 7.00 C 20380 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: 11.94 Conformation dependent library (CDL) restraints added in 9.5 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 32 sheets defined 39.4% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.24 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 48 through 51 removed outlier: 4.071A pdb=" N LEU A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 350 through 371 removed outlier: 3.692A pdb=" N TYR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 385 through 398 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 665 through 677 removed outlier: 4.425A pdb=" N GLU A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'A' and resid 723 through 732 removed outlier: 3.626A pdb=" N LYS A 726 " --> pdb=" O GLU A 723 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 729 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 732 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 793 through 807 removed outlier: 3.654A pdb=" N ALA A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 869 through 877 Processing helix chain 'A' and resid 884 through 895 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 920 through 930 removed outlier: 4.142A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 956 through 965 removed outlier: 3.575A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1002 through 1017 Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 3.797A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1054 removed outlier: 4.460A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1078 removed outlier: 4.064A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 48 through 51 removed outlier: 4.071A pdb=" N LEU B 51 " --> pdb=" O PRO B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 230 through 233 No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 282 through 294 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 350 through 371 removed outlier: 3.692A pdb=" N TYR B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY B 366 " --> pdb=" O ARG B 362 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 385 through 398 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 603 through 616 Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.425A pdb=" N GLU B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 Processing helix chain 'B' and resid 723 through 732 removed outlier: 3.626A pdb=" N LYS B 726 " --> pdb=" O GLU B 723 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 729 " --> pdb=" O LYS B 726 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 732 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 772 through 780 Processing helix chain 'B' and resid 793 through 807 removed outlier: 3.653A pdb=" N ALA B 806 " --> pdb=" O GLU B 802 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 859 through 864 Processing helix chain 'B' and resid 869 through 877 Processing helix chain 'B' and resid 884 through 895 Processing helix chain 'B' and resid 905 through 915 Processing helix chain 'B' and resid 920 through 930 removed outlier: 4.141A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 951 Processing helix chain 'B' and resid 956 through 965 removed outlier: 3.575A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1002 through 1017 Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 3.796A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1054 removed outlier: 4.461A pdb=" N ILE B1052 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B1053 " --> pdb=" O ASP B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1078 removed outlier: 4.064A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1090 No H-bonds generated for 'chain 'B' and resid 1088 through 1090' Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 48 through 51 removed outlier: 4.071A pdb=" N LEU C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 78 through 86 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 230 through 233 No H-bonds generated for 'chain 'C' and resid 230 through 233' Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 282 through 294 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 350 through 371 removed outlier: 3.692A pdb=" N TYR C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY C 366 " --> pdb=" O ARG C 362 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'C' and resid 385 through 398 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 506 through 518 Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 643 through 648 Processing helix chain 'C' and resid 665 through 677 removed outlier: 4.425A pdb=" N GLU C 669 " --> pdb=" O GLY C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 706 Processing helix chain 'C' and resid 723 through 732 removed outlier: 3.626A pdb=" N LYS C 726 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 729 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 732 " --> pdb=" O ARG C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 772 through 780 Processing helix chain 'C' and resid 793 through 807 removed outlier: 3.653A pdb=" N ALA C 806 " --> pdb=" O GLU C 802 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN C 807 " --> pdb=" O ASP C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 869 through 877 Processing helix chain 'C' and resid 884 through 895 Processing helix chain 'C' and resid 905 through 915 Processing helix chain 'C' and resid 920 through 930 removed outlier: 4.142A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 951 Processing helix chain 'C' and resid 956 through 965 removed outlier: 3.575A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1002 through 1017 Processing helix chain 'C' and resid 1025 through 1039 removed outlier: 3.797A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1054 removed outlier: 4.461A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C1053 " --> pdb=" O ASP C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1078 removed outlier: 4.063A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1090 No H-bonds generated for 'chain 'C' and resid 1088 through 1090' Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 48 through 51 removed outlier: 4.072A pdb=" N LEU D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 230 through 233 No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'D' and resid 350 through 371 removed outlier: 3.692A pdb=" N TYR D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY D 366 " --> pdb=" O ARG D 362 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 385 through 398 Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 506 through 518 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 603 through 616 Processing helix chain 'D' and resid 643 through 648 Processing helix chain 'D' and resid 665 through 677 removed outlier: 4.424A pdb=" N GLU D 669 " --> pdb=" O GLY D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 706 Processing helix chain 'D' and resid 723 through 732 removed outlier: 3.626A pdb=" N LYS D 726 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 729 " --> pdb=" O LYS D 726 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 732 " --> pdb=" O ARG D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 772 through 780 Processing helix chain 'D' and resid 793 through 807 removed outlier: 3.653A pdb=" N ALA D 806 " --> pdb=" O GLU D 802 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN D 807 " --> pdb=" O ASP D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 830 Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 869 through 877 Processing helix chain 'D' and resid 884 through 895 Processing helix chain 'D' and resid 905 through 915 Processing helix chain 'D' and resid 920 through 930 removed outlier: 4.142A pdb=" N THR D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 951 Processing helix chain 'D' and resid 956 through 965 removed outlier: 3.575A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1002 through 1017 Processing helix chain 'D' and resid 1025 through 1039 removed outlier: 3.797A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1054 removed outlier: 4.460A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D1053 " --> pdb=" O ASP D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1078 removed outlier: 4.063A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1090 No H-bonds generated for 'chain 'D' and resid 1088 through 1090' Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.775A pdb=" N ALA A 219 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 32 through 34 removed outlier: 4.345A pdb=" N ASN A 54 " --> pdb=" O PHE A 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 92 through 95 Processing sheet with id= D, first strand: chain 'A' and resid 205 through 207 Processing sheet with id= E, first strand: chain 'A' and resid 263 through 268 Processing sheet with id= F, first strand: chain 'A' and resid 275 through 280 removed outlier: 7.048A pdb=" N ILE A 337 " --> pdb=" O TRP A 276 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N MET A 278 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 339 " --> pdb=" O MET A 278 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA A 280 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 341 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 537 through 543 removed outlier: 8.292A pdb=" N ALA A 527 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP A 567 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE A 500 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU A 569 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TRP A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN A 571 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR A 593 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN A 571 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA A 595 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 619 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 596 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 621 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 739 through 744 removed outlier: 3.708A pdb=" N GLY A 717 " --> pdb=" O TRP A 743 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR A 659 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY A 684 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N SER A 661 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA A 686 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 3 through 6 removed outlier: 4.776A pdb=" N ALA B 219 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 32 through 34 removed outlier: 4.344A pdb=" N ASN B 54 " --> pdb=" O PHE B 110 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 92 through 95 Processing sheet with id= L, first strand: chain 'B' and resid 205 through 207 Processing sheet with id= M, first strand: chain 'B' and resid 263 through 268 Processing sheet with id= N, first strand: chain 'B' and resid 275 through 280 removed outlier: 7.048A pdb=" N ILE B 337 " --> pdb=" O TRP B 276 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N MET B 278 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 339 " --> pdb=" O MET B 278 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA B 280 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY B 341 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 537 through 543 removed outlier: 8.292A pdb=" N ALA B 527 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP B 567 " --> pdb=" O LYS B 498 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE B 500 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 569 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TRP B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN B 571 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR B 593 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN B 571 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B 595 " --> pdb=" O ASN B 571 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR B 619 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE B 596 " --> pdb=" O THR B 619 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 621 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 739 through 744 removed outlier: 3.708A pdb=" N GLY B 717 " --> pdb=" O TRP B 743 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR B 659 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY B 684 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N SER B 661 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA B 686 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.776A pdb=" N ALA C 219 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 32 through 34 removed outlier: 4.346A pdb=" N ASN C 54 " --> pdb=" O PHE C 110 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 92 through 95 Processing sheet with id= T, first strand: chain 'C' and resid 205 through 207 Processing sheet with id= U, first strand: chain 'C' and resid 263 through 268 Processing sheet with id= V, first strand: chain 'C' and resid 275 through 280 removed outlier: 7.048A pdb=" N ILE C 337 " --> pdb=" O TRP C 276 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N MET C 278 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 339 " --> pdb=" O MET C 278 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA C 280 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY C 341 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 537 through 543 removed outlier: 8.292A pdb=" N ALA C 527 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP C 567 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE C 500 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU C 569 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TRP C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN C 571 " --> pdb=" O TRP C 502 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR C 593 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN C 571 " --> pdb=" O THR C 593 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA C 595 " --> pdb=" O ASN C 571 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR C 619 " --> pdb=" O ILE C 594 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE C 596 " --> pdb=" O THR C 619 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 621 " --> pdb=" O ILE C 596 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 739 through 744 removed outlier: 3.709A pdb=" N GLY C 717 " --> pdb=" O TRP C 743 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR C 659 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY C 684 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER C 661 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA C 686 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.776A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 32 through 34 removed outlier: 4.345A pdb=" N ASN D 54 " --> pdb=" O PHE D 110 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 92 through 95 Processing sheet with id= AB, first strand: chain 'D' and resid 205 through 207 Processing sheet with id= AC, first strand: chain 'D' and resid 263 through 268 Processing sheet with id= AD, first strand: chain 'D' and resid 275 through 280 removed outlier: 7.048A pdb=" N ILE D 337 " --> pdb=" O TRP D 276 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N MET D 278 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE D 339 " --> pdb=" O MET D 278 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA D 280 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY D 341 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 537 through 543 removed outlier: 8.292A pdb=" N ALA D 527 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 567 " --> pdb=" O LYS D 498 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE D 500 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D 569 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TRP D 502 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN D 571 " --> pdb=" O TRP D 502 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR D 593 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN D 571 " --> pdb=" O THR D 593 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA D 595 " --> pdb=" O ASN D 571 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR D 619 " --> pdb=" O ILE D 594 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE D 596 " --> pdb=" O THR D 619 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE D 621 " --> pdb=" O ILE D 596 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 739 through 744 removed outlier: 3.708A pdb=" N GLY D 717 " --> pdb=" O TRP D 743 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR D 659 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY D 684 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N SER D 661 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA D 686 " --> pdb=" O SER D 661 " (cutoff:3.500A) 1208 hydrogen bonds defined for protein. 3468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.66 Time building geometry restraints manager: 13.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5308 1.30 - 1.43: 8074 1.43 - 1.56: 18899 1.56 - 1.69: 19 1.69 - 1.81: 292 Bond restraints: 32592 Sorted by residual: bond pdb=" C5A ACO B1201 " pdb=" N7A ACO B1201 " ideal model delta sigma weight residual 1.387 1.308 0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C5A ACO A1201 " pdb=" N7A ACO A1201 " ideal model delta sigma weight residual 1.387 1.308 0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C5A ACO D1202 " pdb=" N7A ACO D1202 " ideal model delta sigma weight residual 1.387 1.308 0.079 1.00e-02 1.00e+04 6.20e+01 bond pdb=" C5A ACO C1202 " pdb=" N7A ACO C1202 " ideal model delta sigma weight residual 1.387 1.310 0.077 1.00e-02 1.00e+04 5.97e+01 bond pdb=" C8A ACO D1202 " pdb=" N9A ACO D1202 " ideal model delta sigma weight residual 1.370 1.309 0.061 1.00e-02 1.00e+04 3.69e+01 ... (remaining 32587 not shown) Histogram of bond angle deviations from ideal: 96.36 - 104.32: 587 104.32 - 112.29: 15822 112.29 - 120.25: 14453 120.25 - 128.21: 13062 128.21 - 136.17: 232 Bond angle restraints: 44156 Sorted by residual: angle pdb=" P1A ACO B1201 " pdb=" O3A ACO B1201 " pdb=" P2A ACO B1201 " ideal model delta sigma weight residual 136.83 125.86 10.97 1.00e+00 1.00e+00 1.20e+02 angle pdb=" P1A ACO A1201 " pdb=" O3A ACO A1201 " pdb=" P2A ACO A1201 " ideal model delta sigma weight residual 136.83 126.03 10.80 1.00e+00 1.00e+00 1.17e+02 angle pdb=" P1A ACO D1202 " pdb=" O3A ACO D1202 " pdb=" P2A ACO D1202 " ideal model delta sigma weight residual 136.83 126.13 10.70 1.00e+00 1.00e+00 1.14e+02 angle pdb=" P1A ACO C1202 " pdb=" O3A ACO C1202 " pdb=" P2A ACO C1202 " ideal model delta sigma weight residual 136.83 126.20 10.63 1.00e+00 1.00e+00 1.13e+02 angle pdb=" O3B ACO A1201 " pdb=" P3B ACO A1201 " pdb=" O7A ACO A1201 " ideal model delta sigma weight residual 107.97 99.62 8.35 1.00e+00 1.00e+00 6.98e+01 ... (remaining 44151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.78: 17888 20.78 - 41.56: 1269 41.56 - 62.35: 182 62.35 - 83.13: 37 83.13 - 103.91: 12 Dihedral angle restraints: 19388 sinusoidal: 7748 harmonic: 11640 Sorted by residual: dihedral pdb=" CA ARG B1045 " pdb=" C ARG B1045 " pdb=" N GLU B1046 " pdb=" CA GLU B1046 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG A1045 " pdb=" C ARG A1045 " pdb=" N GLU A1046 " pdb=" CA GLU A1046 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG D1045 " pdb=" C ARG D1045 " pdb=" N GLU D1046 " pdb=" CA GLU D1046 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 19385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3849 0.064 - 0.128: 911 0.128 - 0.192: 112 0.192 - 0.256: 36 0.256 - 0.320: 4 Chirality restraints: 4912 Sorted by residual: chirality pdb=" CB ILE C 123 " pdb=" CA ILE C 123 " pdb=" CG1 ILE C 123 " pdb=" CG2 ILE C 123 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE A 123 " pdb=" CA ILE A 123 " pdb=" CG1 ILE A 123 " pdb=" CG2 ILE A 123 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE D 123 " pdb=" CA ILE D 123 " pdb=" CG1 ILE D 123 " pdb=" CG2 ILE D 123 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 4909 not shown) Planarity restraints: 5652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P ACO D1202 " -0.193 2.00e-02 2.50e+03 1.56e-01 3.03e+02 pdb=" C9P ACO D1202 " 0.075 2.00e-02 2.50e+03 pdb=" CAP ACO D1202 " -0.148 2.00e-02 2.50e+03 pdb=" N8P ACO D1202 " 0.236 2.00e-02 2.50e+03 pdb=" O9P ACO D1202 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO C1202 " 0.189 2.00e-02 2.50e+03 1.52e-01 2.90e+02 pdb=" C9P ACO C1202 " -0.074 2.00e-02 2.50e+03 pdb=" CAP ACO C1202 " 0.145 2.00e-02 2.50e+03 pdb=" N8P ACO C1202 " -0.231 2.00e-02 2.50e+03 pdb=" O9P ACO C1202 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO B1201 " -0.189 2.00e-02 2.50e+03 1.52e-01 2.90e+02 pdb=" C9P ACO B1201 " 0.073 2.00e-02 2.50e+03 pdb=" CAP ACO B1201 " -0.145 2.00e-02 2.50e+03 pdb=" N8P ACO B1201 " 0.230 2.00e-02 2.50e+03 pdb=" O9P ACO B1201 " 0.031 2.00e-02 2.50e+03 ... (remaining 5649 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7282 2.79 - 3.32: 28052 3.32 - 3.84: 54182 3.84 - 4.37: 62542 4.37 - 4.90: 109298 Nonbonded interactions: 261356 Sorted by model distance: nonbonded pdb=" O ASN D 671 " pdb=" OG SER D 675 " model vdw 2.260 2.440 nonbonded pdb=" O ASN B 671 " pdb=" OG SER B 675 " model vdw 2.260 2.440 nonbonded pdb=" O ASN A 671 " pdb=" OG SER A 675 " model vdw 2.260 2.440 nonbonded pdb=" O ASN C 671 " pdb=" OG SER C 675 " model vdw 2.260 2.440 nonbonded pdb=" O LYS A 265 " pdb=" OH TYR A 319 " model vdw 2.289 2.440 ... (remaining 261351 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 'A' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 180 5.16 5 C 20380 2.51 5 N 5388 2.21 5 O 5940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 5.390 Check model and map are aligned: 0.460 Convert atoms to be neutral: 0.270 Process input model: 101.740 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.006 0.104 32592 Z= 0.378 Angle : 0.958 19.773 44156 Z= 0.556 Chirality : 0.057 0.320 4912 Planarity : 0.008 0.156 5652 Dihedral : 14.546 103.910 11996 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.37 (0.11), residues: 4068 helix: -1.73 (0.10), residues: 1708 sheet: -0.18 (0.22), residues: 588 loop : -1.79 (0.13), residues: 1772 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 367 time to evaluate : 3.757 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 379 average time/residue: 1.3522 time to fit residues: 614.7563 Evaluate side-chains 273 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 262 time to evaluate : 3.524 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 3 average time/residue: 0.3129 time to fit residues: 7.4057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 50.0000 chunk 208 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 319 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 194 optimal weight: 0.0070 chunk 238 optimal weight: 10.0000 chunk 370 optimal weight: 3.9990 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 32592 Z= 0.391 Angle : 0.656 10.922 44156 Z= 0.337 Chirality : 0.048 0.175 4912 Planarity : 0.005 0.064 5652 Dihedral : 6.911 98.144 4496 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.65 (0.12), residues: 4068 helix: -0.84 (0.12), residues: 1740 sheet: -0.32 (0.23), residues: 564 loop : -1.51 (0.14), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 274 time to evaluate : 3.608 Fit side-chains outliers start: 50 outliers final: 18 residues processed: 300 average time/residue: 1.1433 time to fit residues: 426.3445 Evaluate side-chains 272 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 254 time to evaluate : 3.722 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.5112 time to fit residues: 7.7055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 50.0000 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 40.0000 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 30.0000 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 297 optimal weight: 0.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN ** D 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.008 0.086 32592 Z= 0.512 Angle : 0.714 10.485 44156 Z= 0.363 Chirality : 0.051 0.185 4912 Planarity : 0.005 0.058 5652 Dihedral : 6.954 95.636 4496 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.13), residues: 4068 helix: -0.79 (0.12), residues: 1752 sheet: -0.48 (0.23), residues: 556 loop : -1.38 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 258 time to evaluate : 3.818 Fit side-chains outliers start: 56 outliers final: 30 residues processed: 287 average time/residue: 1.2350 time to fit residues: 433.2966 Evaluate side-chains 266 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 236 time to evaluate : 3.651 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 20 residues processed: 13 average time/residue: 0.9556 time to fit residues: 20.9994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 6.9990 chunk 279 optimal weight: 0.0060 chunk 192 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 chunk 249 optimal weight: 0.7980 chunk 372 optimal weight: 2.9990 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 30.0000 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN C 777 GLN C 879 GLN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 GLN D 879 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 32592 Z= 0.154 Angle : 0.546 11.868 44156 Z= 0.277 Chirality : 0.043 0.146 4912 Planarity : 0.004 0.050 5652 Dihedral : 6.261 86.805 4496 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.06 (0.13), residues: 4068 helix: -0.16 (0.12), residues: 1736 sheet: -0.36 (0.23), residues: 556 loop : -1.28 (0.14), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 255 time to evaluate : 3.536 Fit side-chains outliers start: 43 outliers final: 21 residues processed: 281 average time/residue: 1.2842 time to fit residues: 440.0563 Evaluate side-chains 254 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 233 time to evaluate : 3.235 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.6010 time to fit residues: 9.8845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 30.0000 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 201 optimal weight: 2.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 32592 Z= 0.388 Angle : 0.636 11.962 44156 Z= 0.321 Chirality : 0.047 0.156 4912 Planarity : 0.004 0.047 5652 Dihedral : 6.353 86.553 4496 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.08 (0.13), residues: 4068 helix: -0.22 (0.12), residues: 1748 sheet: -0.36 (0.24), residues: 556 loop : -1.25 (0.14), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 236 time to evaluate : 3.522 Fit side-chains outliers start: 58 outliers final: 27 residues processed: 276 average time/residue: 1.2640 time to fit residues: 427.1028 Evaluate side-chains 254 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 3.487 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 22 residues processed: 5 average time/residue: 0.8278 time to fit residues: 10.6176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 40.0000 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 231 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 40.0000 chunk 182 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 32592 Z= 0.205 Angle : 0.565 11.603 44156 Z= 0.285 Chirality : 0.044 0.243 4912 Planarity : 0.004 0.042 5652 Dihedral : 6.051 84.773 4496 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 4068 helix: 0.05 (0.12), residues: 1736 sheet: -0.32 (0.24), residues: 556 loop : -1.20 (0.14), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 3.705 Fit side-chains outliers start: 39 outliers final: 27 residues processed: 265 average time/residue: 1.3328 time to fit residues: 430.4724 Evaluate side-chains 253 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 226 time to evaluate : 3.530 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 7 average time/residue: 0.7932 time to fit residues: 12.5098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 224 optimal weight: 0.0970 chunk 288 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 332 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 393 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN D 777 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 32592 Z= 0.264 Angle : 0.584 11.767 44156 Z= 0.294 Chirality : 0.045 0.218 4912 Planarity : 0.004 0.042 5652 Dihedral : 5.990 83.913 4496 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4068 helix: 0.06 (0.12), residues: 1740 sheet: -0.32 (0.24), residues: 560 loop : -1.13 (0.14), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 3.529 Fit side-chains outliers start: 39 outliers final: 25 residues processed: 263 average time/residue: 1.2933 time to fit residues: 414.4690 Evaluate side-chains 249 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 224 time to evaluate : 3.503 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 1.3758 time to fit residues: 6.8498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.2231 > 50: distance: 86 - 95: 28.126 distance: 95 - 96: 18.034 distance: 96 - 97: 46.822 distance: 96 - 99: 50.407 distance: 97 - 98: 24.516 distance: 97 - 103: 18.633 distance: 99 - 100: 36.122 distance: 100 - 102: 34.809 distance: 103 - 104: 22.889 distance: 104 - 105: 42.029 distance: 104 - 107: 38.012 distance: 105 - 106: 5.545 distance: 105 - 112: 22.152 distance: 107 - 108: 37.754 distance: 108 - 109: 19.425 distance: 109 - 111: 64.707 distance: 112 - 113: 20.325 distance: 112 - 118: 14.713 distance: 113 - 114: 39.843 distance: 113 - 116: 33.314 distance: 114 - 115: 20.974 distance: 114 - 119: 23.045 distance: 116 - 117: 31.928 distance: 117 - 118: 37.899 distance: 119 - 120: 22.190 distance: 120 - 121: 23.166 distance: 120 - 123: 21.786 distance: 121 - 122: 21.610 distance: 121 - 125: 17.401 distance: 123 - 124: 26.292 distance: 125 - 126: 15.063 distance: 126 - 127: 4.584 distance: 126 - 129: 40.690 distance: 127 - 128: 25.083 distance: 127 - 132: 14.919 distance: 129 - 130: 12.945 distance: 129 - 131: 20.392 distance: 132 - 133: 34.225 distance: 133 - 134: 34.570 distance: 133 - 136: 12.715 distance: 134 - 135: 12.275 distance: 134 - 137: 28.150 distance: 137 - 138: 13.824 distance: 138 - 139: 21.960 distance: 138 - 141: 20.294 distance: 139 - 140: 30.742 distance: 139 - 142: 8.653 distance: 142 - 143: 21.813 distance: 142 - 213: 21.308 distance: 143 - 144: 18.666 distance: 143 - 146: 22.065 distance: 144 - 145: 18.975 distance: 144 - 150: 13.738 distance: 145 - 224: 7.640 distance: 146 - 147: 9.806 distance: 147 - 148: 6.700 distance: 148 - 149: 10.150 distance: 150 - 151: 20.942 distance: 151 - 152: 30.057 distance: 151 - 154: 21.562 distance: 152 - 153: 13.593 distance: 152 - 157: 17.902 distance: 154 - 155: 36.996 distance: 154 - 156: 14.843 distance: 157 - 158: 8.222 distance: 158 - 159: 29.565 distance: 158 - 161: 17.858 distance: 159 - 160: 19.843 distance: 159 - 169: 26.946 distance: 161 - 162: 18.655 distance: 162 - 163: 11.122 distance: 162 - 164: 16.170 distance: 163 - 165: 10.785 distance: 164 - 166: 7.771 distance: 165 - 167: 17.315 distance: 166 - 167: 15.153 distance: 167 - 168: 6.658