Starting phenix.real_space_refine on Wed Feb 21 21:03:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/02_2024/7lla_23413_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/02_2024/7lla_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_23413/02_2024/7lla_23413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/02_2024/7lla_23413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/02_2024/7lla_23413_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lla_23413/02_2024/7lla_23413_updated.pdb" } resolution = 2.97 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= 0.008 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 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. 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 30.32, per 1000 atoms: 0.95 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: 16.24 Conformation dependent library (CDL) restraints added in 13.5 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: 8.52 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: 12.56 Time building geometry restraints manager: 16.74 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: 17984 20.78 - 41.56: 1306 41.56 - 62.35: 206 62.35 - 83.13: 44 83.13 - 103.91: 12 Dihedral angle restraints: 19552 sinusoidal: 7912 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 19549 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 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: 0.730 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: 4.230 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 117.050 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 14.873 103.910 12160 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.59 % Allowed : 0.89 % Favored : 98.52 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 743 HIS 0.006 0.001 HIS A 997 PHE 0.018 0.002 PHE A 197 TYR 0.017 0.002 TYR A 124 ARG 0.015 0.001 ARG D1078 *********************** 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 : 3.310 Fit side-chains REVERT: B 614 ASP cc_start: 0.7531 (m-30) cc_final: 0.7309 (m-30) REVERT: C 491 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (t) REVERT: D 496 HIS cc_start: 0.7534 (m-70) cc_final: 0.7321 (m90) outliers start: 20 outliers final: 11 residues processed: 379 average time/residue: 1.3945 time to fit residues: 627.1910 Evaluate side-chains 273 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 261 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 834 ILE 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** B1086 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 32592 Z= 0.384 Angle : 0.655 11.091 44156 Z= 0.336 Chirality : 0.048 0.174 4912 Planarity : 0.005 0.064 5652 Dihedral : 8.606 102.681 4683 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.43 % Allowed : 9.23 % Favored : 89.34 % 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: -0.83 (0.12), residues: 1740 sheet: -0.33 (0.23), residues: 564 loop : -1.52 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 233 HIS 0.005 0.001 HIS D1086 PHE 0.018 0.002 PHE A 197 TYR 0.020 0.002 TYR D 885 ARG 0.012 0.001 ARG C 703 *********************** 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 326 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 278 time to evaluate : 3.480 Fit side-chains REVERT: A 491 THR cc_start: 0.8597 (m) cc_final: 0.8368 (t) REVERT: B 614 ASP cc_start: 0.7931 (m-30) cc_final: 0.7666 (m-30) REVERT: C 197 PHE cc_start: 0.8355 (m-10) cc_final: 0.8153 (m-10) outliers start: 48 outliers final: 15 residues processed: 302 average time/residue: 1.2294 time to fit residues: 451.9295 Evaluate side-chains 268 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 253 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 728 CYS Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 728 CYS Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 954 ILE 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: 8.9990 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: 3.9990 chunk 330 optimal weight: 0.0970 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 0.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- 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** B1086 HIS C 705 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 32592 Z= 0.372 Angle : 0.634 9.802 44156 Z= 0.323 Chirality : 0.047 0.180 4912 Planarity : 0.005 0.059 5652 Dihedral : 8.101 92.831 4668 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.48 % Allowed : 10.75 % Favored : 87.77 % 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: -1.40 (0.13), residues: 4068 helix: -0.58 (0.12), residues: 1744 sheet: -0.37 (0.23), residues: 556 loop : -1.37 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 743 HIS 0.005 0.001 HIS C 975 PHE 0.018 0.002 PHE B 697 TYR 0.025 0.002 TYR B 16 ARG 0.010 0.001 ARG B 703 *********************** 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 303 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 253 time to evaluate : 3.287 Fit side-chains REVERT: A 712 MET cc_start: 0.8277 (ptp) cc_final: 0.8003 (ptm) REVERT: B 1024 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7719 (m-40) REVERT: C 391 MET cc_start: 0.7418 (mmm) cc_final: 0.7135 (mmm) REVERT: C 556 MET cc_start: 0.8333 (ttp) cc_final: 0.8106 (ttp) outliers start: 50 outliers final: 24 residues processed: 277 average time/residue: 1.3718 time to fit residues: 454.5954 Evaluate side-chains 268 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 243 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1036 MET Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 545 HIS Chi-restraints excluded: chain C residue 726 LYS Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 1036 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 192 optimal weight: 0.0570 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 372 optimal weight: 10.0000 chunk 394 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 353 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 B 879 GLN ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN C 879 GLN D 777 GLN D 879 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32592 Z= 0.157 Angle : 0.535 12.212 44156 Z= 0.271 Chirality : 0.043 0.150 4912 Planarity : 0.004 0.049 5652 Dihedral : 7.255 84.311 4668 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.31 % Allowed : 11.97 % Favored : 86.73 % 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: -1.00 (0.13), residues: 4068 helix: -0.10 (0.12), residues: 1736 sheet: -0.30 (0.23), residues: 556 loop : -1.26 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 743 HIS 0.002 0.000 HIS A 135 PHE 0.017 0.001 PHE B 354 TYR 0.013 0.001 TYR B 124 ARG 0.010 0.000 ARG A1045 *********************** 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 296 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 252 time to evaluate : 3.684 Fit side-chains REVERT: A 376 PHE cc_start: 0.6629 (m-80) cc_final: 0.6309 (m-10) REVERT: A 712 MET cc_start: 0.8217 (ptp) cc_final: 0.7978 (ptm) REVERT: B 1024 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.7359 (m110) outliers start: 44 outliers final: 15 residues processed: 276 average time/residue: 1.3129 time to fit residues: 438.2217 Evaluate side-chains 248 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 30.0000 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 201 optimal weight: 4.9990 chunk 353 optimal weight: 0.1980 chunk 99 optimal weight: 7.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- 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 ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN D 777 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32592 Z= 0.286 Angle : 0.580 10.903 44156 Z= 0.294 Chirality : 0.045 0.163 4912 Planarity : 0.004 0.045 5652 Dihedral : 7.135 81.486 4660 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.45 % Allowed : 12.38 % Favored : 86.16 % 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: -0.90 (0.13), residues: 4068 helix: -0.03 (0.12), residues: 1744 sheet: -0.27 (0.23), residues: 556 loop : -1.20 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 827 HIS 0.003 0.001 HIS C 975 PHE 0.016 0.001 PHE B 354 TYR 0.025 0.002 TYR B 16 ARG 0.006 0.000 ARG D 703 *********************** 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 291 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 242 time to evaluate : 3.474 Fit side-chains revert: symmetry clash REVERT: A 376 PHE cc_start: 0.6737 (m-80) cc_final: 0.6419 (m-10) REVERT: A 712 MET cc_start: 0.8293 (ptp) cc_final: 0.8038 (ptm) REVERT: B 1024 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7604 (m110) outliers start: 49 outliers final: 24 residues processed: 277 average time/residue: 1.2882 time to fit residues: 432.0812 Evaluate side-chains 257 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 232 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 7.9990 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 40.0000 chunk 182 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN D 777 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32592 Z= 0.236 Angle : 0.570 11.859 44156 Z= 0.287 Chirality : 0.045 0.186 4912 Planarity : 0.004 0.042 5652 Dihedral : 6.968 77.293 4660 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.10 % Allowed : 13.24 % Favored : 85.66 % 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: -0.81 (0.13), residues: 4068 helix: 0.08 (0.12), residues: 1740 sheet: -0.24 (0.23), residues: 556 loop : -1.18 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 276 HIS 0.003 0.001 HIS C 410 PHE 0.017 0.001 PHE A 354 TYR 0.014 0.001 TYR B 304 ARG 0.005 0.000 ARG D 703 *********************** 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 265 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 228 time to evaluate : 3.364 Fit side-chains REVERT: A 376 PHE cc_start: 0.6747 (m-80) cc_final: 0.6412 (m-10) REVERT: A 712 MET cc_start: 0.8239 (ptp) cc_final: 0.7983 (ptm) REVERT: B 1024 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7569 (m110) REVERT: D 391 MET cc_start: 0.7453 (mmm) cc_final: 0.7111 (mmm) outliers start: 37 outliers final: 27 residues processed: 257 average time/residue: 1.2838 time to fit residues: 399.5156 Evaluate side-chains 249 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 224 optimal weight: 30.0000 chunk 288 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 332 optimal weight: 50.0000 chunk 220 optimal weight: 0.6980 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN ** C 303 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32592 Z= 0.245 Angle : 0.573 11.958 44156 Z= 0.287 Chirality : 0.045 0.212 4912 Planarity : 0.004 0.041 5652 Dihedral : 6.873 73.152 4660 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.19 % Allowed : 13.60 % Favored : 85.21 % 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: -0.76 (0.13), residues: 4068 helix: 0.13 (0.12), residues: 1740 sheet: -0.23 (0.24), residues: 556 loop : -1.15 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 233 HIS 0.002 0.001 HIS C 537 PHE 0.017 0.001 PHE A 354 TYR 0.023 0.001 TYR B 16 ARG 0.004 0.000 ARG D 703 *********************** 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: 40 poor density : 229 time to evaluate : 3.550 Fit side-chains REVERT: A 376 PHE cc_start: 0.6808 (m-80) cc_final: 0.6579 (m-10) REVERT: A 712 MET cc_start: 0.8254 (ptp) cc_final: 0.7994 (ptm) REVERT: B 1024 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7604 (m110) REVERT: D 391 MET cc_start: 0.7493 (mmm) cc_final: 0.7208 (mmm) outliers start: 40 outliers final: 28 residues processed: 260 average time/residue: 1.3660 time to fit residues: 427.2256 Evaluate side-chains 249 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 0.0570 chunk 76 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 267 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 309 optimal weight: 7.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN ** C 303 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32592 Z= 0.154 Angle : 0.541 12.131 44156 Z= 0.270 Chirality : 0.043 0.179 4912 Planarity : 0.004 0.039 5652 Dihedral : 6.523 65.676 4660 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.07 % Allowed : 14.10 % Favored : 84.83 % 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: -0.55 (0.13), residues: 4068 helix: 0.33 (0.13), residues: 1740 sheet: -0.18 (0.24), residues: 560 loop : -1.05 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 276 HIS 0.002 0.000 HIS C 997 PHE 0.015 0.001 PHE A 354 TYR 0.013 0.001 TYR C 307 ARG 0.004 0.000 ARG D 703 *********************** REFINEMENT MACRO_CYCLE 8 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 263 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 3.828 Fit side-chains REVERT: A 376 PHE cc_start: 0.6637 (m-80) cc_final: 0.6384 (m-80) REVERT: B 698 MET cc_start: 0.7188 (tpt) cc_final: 0.6945 (mmm) REVERT: D 391 MET cc_start: 0.7414 (mmm) cc_final: 0.7043 (mmm) outliers start: 36 outliers final: 23 residues processed: 255 average time/residue: 1.4536 time to fit residues: 441.7147 Evaluate side-chains 237 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 777 GLN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 777 GLN Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 10.0000 chunk 376 optimal weight: 7.9990 chunk 343 optimal weight: 6.9990 chunk 366 optimal weight: 8.9990 chunk 220 optimal weight: 0.0170 chunk 159 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 365 optimal weight: 9.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- 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 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN D 777 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32592 Z= 0.222 Angle : 0.571 12.394 44156 Z= 0.283 Chirality : 0.045 0.296 4912 Planarity : 0.004 0.040 5652 Dihedral : 6.545 66.622 4660 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.16 % Allowed : 14.34 % Favored : 84.50 % 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: -0.47 (0.13), residues: 4068 helix: 0.38 (0.13), residues: 1724 sheet: -0.13 (0.24), residues: 560 loop : -0.99 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 233 HIS 0.002 0.000 HIS C 537 PHE 0.017 0.001 PHE A 354 TYR 0.026 0.001 TYR B 16 ARG 0.009 0.000 ARG A 521 *********************** REFINEMENT MACRO_CYCLE 9 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 259 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 3.494 Fit side-chains REVERT: A 376 PHE cc_start: 0.6724 (m-80) cc_final: 0.6438 (m-10) REVERT: A 698 MET cc_start: 0.7155 (mmm) cc_final: 0.5905 (mmm) REVERT: C 777 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: D 391 MET cc_start: 0.7446 (mmm) cc_final: 0.7071 (mmm) outliers start: 39 outliers final: 29 residues processed: 253 average time/residue: 1.3579 time to fit residues: 412.7462 Evaluate side-chains 241 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 777 GLN Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 777 GLN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 954 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 6.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 0.0970 chunk 374 optimal weight: 30.0000 chunk 323 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 GLN ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN D 777 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32592 Z= 0.212 Angle : 0.577 12.606 44156 Z= 0.286 Chirality : 0.044 0.296 4912 Planarity : 0.004 0.039 5652 Dihedral : 6.532 66.185 4660 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.98 % Allowed : 14.88 % Favored : 84.14 % 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: -0.47 (0.13), residues: 4068 helix: 0.38 (0.13), residues: 1724 sheet: -0.11 (0.24), residues: 560 loop : -1.00 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 276 HIS 0.002 0.000 HIS C 975 PHE 0.018 0.001 PHE B 354 TYR 0.024 0.001 TYR A 16 ARG 0.004 0.000 ARG D 703 ********************** REFINEMENT MACRO_CYCLE 10 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 249 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 3.496 Fit side-chains REVERT: A 376 PHE cc_start: 0.6743 (m-80) cc_final: 0.6429 (m-80) REVERT: D 391 MET cc_start: 0.7419 (mmm) cc_final: 0.7039 (mmm) REVERT: D 698 MET cc_start: 0.7183 (mmm) cc_final: 0.5875 (mmm) outliers start: 33 outliers final: 28 residues processed: 243 average time/residue: 1.4132 time to fit residues: 410.8192 Evaluate side-chains 238 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1024 ASN Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 777 GLN Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 925 THR Chi-restraints excluded: chain D residue 933 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 324 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 332 optimal weight: 30.0000 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 777 GLN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN D 777 GLN D1024 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.195510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114651 restraints weight = 71215.587| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 4.85 r_work: 0.3084 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2915 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= 0.406 Angle : 0.660 12.671 44156 Z= 0.328 Chirality : 0.048 0.374 4912 Planarity : 0.004 0.042 5652 Dihedral : 6.924 67.655 4660 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.13 % Allowed : 14.67 % Favored : 84.20 % 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: -0.74 (0.13), residues: 4068 helix: 0.06 (0.12), residues: 1740 sheet: -0.16 (0.24), residues: 560 loop : -1.07 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 877 HIS 0.004 0.001 HIS D 975 PHE 0.021 0.002 PHE B 354 TYR 0.023 0.002 TYR B 16 ARG 0.005 0.000 ARG D 703 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9326.03 seconds wall clock time: 168 minutes 30.58 seconds (10110.58 seconds total)