Starting phenix.real_space_refine on Sun Aug 24 05:04:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8goo_34178/08_2025/8goo_34178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8goo_34178/08_2025/8goo_34178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8goo_34178/08_2025/8goo_34178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8goo_34178/08_2025/8goo_34178.map" model { file = "/net/cci-nas-00/data/ceres_data/8goo_34178/08_2025/8goo_34178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8goo_34178/08_2025/8goo_34178.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 15 5.49 5 S 36 5.16 5 C 10741 2.51 5 N 2894 2.21 5 O 3280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16966 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2725 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2725 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2717 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 95 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "U" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 95 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 95 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.03, per 1000 atoms: 0.24 Number of scatterers: 16966 At special positions: 0 Unit cell: (188.554, 188.554, 98.6473, 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 36 16.00 P 15 15.00 O 3280 8.00 N 2894 7.00 C 10741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.03 Simple disulfide: pdb=" SG CYS M 150 " - pdb=" SG CYS M 206 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.23 Conformation dependent library (CDL) restraints added in 796.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 45 sheets defined 5.5% alpha, 44.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.000A pdb=" N ARG A 283 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 279 through 283 removed outlier: 4.000A pdb=" N ARG B 283 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.999A pdb=" N ARG C 283 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.662A pdb=" N LYS D 68 " --> pdb=" O ASP D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.818A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 removed outlier: 3.548A pdb=" N GLY E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.858A pdb=" N HIS E 190 " --> pdb=" O ASP E 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.663A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.819A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.548A pdb=" N GLY L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.859A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 68 removed outlier: 3.661A pdb=" N LYS M 68 " --> pdb=" O ASP M 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 65 through 68' Processing helix chain 'M' and resid 90 through 94 removed outlier: 3.818A pdb=" N THR M 94 " --> pdb=" O ALA M 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 129 removed outlier: 3.548A pdb=" N GLY N 129 " --> pdb=" O GLN N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 190 removed outlier: 3.858A pdb=" N HIS N 190 " --> pdb=" O ASP N 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 3.520A pdb=" N VAL A 38 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL A 9 " --> pdb=" O TPO G 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 5.908A pdb=" N PHE A 28 " --> pdb=" O VAL A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 88 removed outlier: 6.662A pdb=" N ASP A 79 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A 62 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 81 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 54 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 88 removed outlier: 6.662A pdb=" N ASP A 79 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A 62 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 81 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 54 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 128 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 190 Processing sheet with id=AA6, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.713A pdb=" N TYR A 209 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 232 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.520A pdb=" N VAL B 38 " --> pdb=" O PHE B 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 30 removed outlier: 5.908A pdb=" N PHE B 28 " --> pdb=" O VAL B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 88 removed outlier: 6.661A pdb=" N ASP B 79 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE B 62 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 81 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 54 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 78 through 88 removed outlier: 6.661A pdb=" N ASP B 79 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE B 62 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 81 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 54 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 128 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 190 Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.713A pdb=" N TYR B 209 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 336 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU B 344 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N VAL B 320 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 232 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 255 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 113 through 118 removed outlier: 3.520A pdb=" N VAL C 38 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 9 " --> pdb=" O TPO V 339 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG V 337 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.909A pdb=" N PHE C 28 " --> pdb=" O VAL C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 78 through 88 removed outlier: 6.663A pdb=" N ASP C 79 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE C 62 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 81 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 54 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 88 removed outlier: 6.663A pdb=" N ASP C 79 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE C 62 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 81 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 54 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 128 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 184 through 190 Processing sheet with id=AB9, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.714A pdb=" N TYR C 209 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 336 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU C 344 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N VAL C 320 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 232 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA C 255 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA C 240 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS C 251 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 242 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLN C 249 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.528A pdb=" N GLN D 6 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 28 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET D 86 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 13 through 15 removed outlier: 4.237A pdb=" N GLY D 13 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 120 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N SER D 35 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER D 55 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 13 through 15 removed outlier: 4.237A pdb=" N GLY D 13 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 120 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 130 through 134 removed outlier: 6.078A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N SER D 189 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL D 191 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR D 175 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AC6, first strand: chain 'E' and resid 5 through 8 removed outlier: 4.622A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 76 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.787A pdb=" N GLU E 106 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.578A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN E 91 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.733A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.528A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET H 86 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 13 through 15 removed outlier: 4.238A pdb=" N GLY H 13 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR H 120 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 13 through 15 removed outlier: 4.238A pdb=" N GLY H 13 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR H 120 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.078A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N SER H 189 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL H 191 " --> pdb=" O THR H 175 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR H 175 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 161 through 163 Processing sheet with id=AD6, first strand: chain 'L' and resid 5 through 8 removed outlier: 4.621A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE L 76 " --> pdb=" O VAL L 20 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 12 through 14 removed outlier: 3.787A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.577A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.734A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 6 through 10 removed outlier: 3.527A pdb=" N GLN M 6 " --> pdb=" O SER M 28 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER M 28 " --> pdb=" O GLN M 6 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL M 8 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET M 86 " --> pdb=" O LEU M 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR M 81 " --> pdb=" O ASP M 76 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 13 through 15 removed outlier: 4.237A pdb=" N GLY M 13 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR M 120 " --> pdb=" O GLY M 13 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N SER M 35 " --> pdb=" O SER M 55 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER M 55 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE M 37 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TRP M 39 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 13 through 15 removed outlier: 4.237A pdb=" N GLY M 13 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR M 120 " --> pdb=" O GLY M 13 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR M 112 " --> pdb=" O ARG M 101 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 130 through 134 removed outlier: 6.078A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N SER M 189 " --> pdb=" O PRO M 177 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL M 191 " --> pdb=" O THR M 175 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR M 175 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 161 through 163 Processing sheet with id=AE6, first strand: chain 'N' and resid 5 through 8 removed outlier: 4.623A pdb=" N VAL N 20 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE N 76 " --> pdb=" O VAL N 20 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 12 through 14 removed outlier: 3.788A pdb=" N GLU N 106 " --> pdb=" O LEU N 12 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.578A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN N 91 " --> pdb=" O THR N 98 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR N 98 " --> pdb=" O GLN N 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 115 through 119 removed outlier: 3.734A pdb=" N ASN N 138 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR N 174 " --> pdb=" O ASN N 139 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1773 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: 2.82 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5463 1.35 - 1.46: 4075 1.46 - 1.58: 7742 1.58 - 1.70: 37 1.70 - 1.81: 48 Bond restraints: 17365 Sorted by residual: bond pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" OG1 TPO G 342 " pdb=" P TPO G 342 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" OG1 TPO G 339 " pdb=" P TPO G 339 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 17360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 23269 2.31 - 4.61: 337 4.61 - 6.92: 48 6.92 - 9.23: 14 9.23 - 11.53: 5 Bond angle restraints: 23673 Sorted by residual: angle pdb=" N GLU B 339 " pdb=" CA GLU B 339 " pdb=" C GLU B 339 " ideal model delta sigma weight residual 109.85 117.22 -7.37 1.58e+00 4.01e-01 2.18e+01 angle pdb=" CA GLU B 339 " pdb=" C GLU B 339 " pdb=" O GLU B 339 " ideal model delta sigma weight residual 121.46 116.63 4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" N GLU B 339 " pdb=" CA GLU B 339 " pdb=" CB GLU B 339 " ideal model delta sigma weight residual 111.20 104.69 6.51 1.62e+00 3.81e-01 1.62e+01 angle pdb=" CB TPO G 339 " pdb=" OG1 TPO G 339 " pdb=" P TPO G 339 " ideal model delta sigma weight residual 119.31 107.78 11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C LEU A 49 " pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 ... (remaining 23668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 9490 17.54 - 35.07: 799 35.07 - 52.61: 90 52.61 - 70.14: 12 70.14 - 87.68: 12 Dihedral angle restraints: 10403 sinusoidal: 3920 harmonic: 6483 Sorted by residual: dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N ARG A 96 " pdb=" CA ARG A 96 " ideal model delta harmonic sigma weight residual 0.00 -33.16 33.16 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA PRO B 95 " pdb=" C PRO B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 0.00 -33.16 33.16 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA PRO C 95 " pdb=" C PRO C 95 " pdb=" N ARG C 96 " pdb=" CA ARG C 96 " ideal model delta harmonic sigma weight residual 0.00 -33.10 33.10 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 10400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1963 0.040 - 0.079: 434 0.079 - 0.119: 265 0.119 - 0.159: 22 0.159 - 0.199: 7 Chirality restraints: 2691 Sorted by residual: chirality pdb=" CB TPO V 342 " pdb=" CA TPO V 342 " pdb=" OG1 TPO V 342 " pdb=" CG2 TPO V 342 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CA VAL V 340 " pdb=" N VAL V 340 " pdb=" C VAL V 340 " pdb=" CB VAL V 340 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CB TPO U 342 " pdb=" CA TPO U 342 " pdb=" OG1 TPO U 342 " pdb=" CG2 TPO U 342 " both_signs ideal model delta sigma weight residual False 2.48 2.67 -0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 2688 not shown) Planarity restraints: 3032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 91 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 92 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 92 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 92 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 91 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 92 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 91 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO C 92 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 92 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 92 " -0.026 5.00e-02 4.00e+02 ... (remaining 3029 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1807 2.76 - 3.29: 16318 3.29 - 3.83: 27281 3.83 - 4.36: 29805 4.36 - 4.90: 52894 Nonbonded interactions: 128105 Sorted by model distance: nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.221 3.040 nonbonded pdb=" OG SER E 64 " pdb=" OG1 THR E 75 " model vdw 2.221 3.040 nonbonded pdb=" OG SER N 64 " pdb=" OG1 THR N 75 " model vdw 2.221 3.040 nonbonded pdb=" O GLY B 212 " pdb=" ND2 ASN H 31 " model vdw 2.240 3.120 nonbonded pdb=" OG SER N 8 " pdb=" OG1 THR N 23 " model vdw 2.255 3.040 ... (remaining 128100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 350)) selection = (chain 'B' and (resid 7 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 350)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'U' selection = chain 'V' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.040 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 17374 Z= 0.222 Angle : 0.659 11.533 23691 Z= 0.308 Chirality : 0.044 0.199 2691 Planarity : 0.004 0.047 3032 Dihedral : 12.857 87.676 6194 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Rotamer: Outliers : 0.49 % Allowed : 0.66 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 2157 helix: 2.06 (0.61), residues: 78 sheet: 1.28 (0.17), residues: 996 loop : -0.63 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.007 0.001 TYR N 174 PHE 0.009 0.001 PHE M 30 TRP 0.004 0.001 TRP E 36 HIS 0.002 0.000 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00446 (17365) covalent geometry : angle 0.65953 (23673) SS BOND : bond 0.00113 ( 9) SS BOND : angle 0.34473 ( 18) hydrogen bonds : bond 0.25690 ( 590) hydrogen bonds : angle 9.34508 ( 1773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.8558 (t0) cc_final: 0.8194 (t0) REVERT: H 31 ASN cc_start: 0.8440 (t0) cc_final: 0.7957 (t0) REVERT: M 31 ASN cc_start: 0.8513 (t0) cc_final: 0.7925 (t0) REVERT: N 94 TYR cc_start: 0.8285 (m-80) cc_final: 0.7894 (m-10) REVERT: N 137 LEU cc_start: 0.8941 (mm) cc_final: 0.8708 (mm) outliers start: 9 outliers final: 3 residues processed: 109 average time/residue: 0.1256 time to fit residues: 21.0293 Evaluate side-chains 78 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0980 chunk 200 optimal weight: 0.0020 chunk 212 optimal weight: 5.9990 overall best weight: 2.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN N 125 GLN ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.063288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044082 restraints weight = 117575.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.045362 restraints weight = 73234.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046191 restraints weight = 55234.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046697 restraints weight = 46475.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.046876 restraints weight = 41890.421| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17374 Z= 0.237 Angle : 0.687 7.337 23691 Z= 0.355 Chirality : 0.045 0.192 2691 Planarity : 0.005 0.047 3032 Dihedral : 5.365 49.779 2427 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 0.16 % Allowed : 7.30 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2157 helix: 2.04 (0.59), residues: 78 sheet: 0.87 (0.17), residues: 957 loop : -0.75 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 67 TYR 0.018 0.002 TYR M 98 PHE 0.014 0.002 PHE L 99 TRP 0.007 0.002 TRP N 36 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00516 (17365) covalent geometry : angle 0.68641 (23673) SS BOND : bond 0.00682 ( 9) SS BOND : angle 1.15996 ( 18) hydrogen bonds : bond 0.04282 ( 590) hydrogen bonds : angle 6.44221 ( 1773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8808 (ppp) cc_final: 0.8564 (ppp) REVERT: B 141 LEU cc_start: 0.9288 (pt) cc_final: 0.9072 (mt) REVERT: D 31 ASN cc_start: 0.8952 (t0) cc_final: 0.8560 (t0) REVERT: D 214 ASN cc_start: 0.8919 (m-40) cc_final: 0.8698 (m-40) REVERT: H 31 ASN cc_start: 0.8815 (t0) cc_final: 0.8438 (t0) REVERT: H 73 ILE cc_start: 0.9104 (tp) cc_final: 0.8823 (pt) REVERT: M 31 ASN cc_start: 0.9019 (t0) cc_final: 0.8574 (t0) REVERT: M 214 ASN cc_start: 0.8833 (m-40) cc_final: 0.8625 (m-40) REVERT: N 137 LEU cc_start: 0.8938 (mm) cc_final: 0.8676 (mm) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 0.0995 time to fit residues: 14.4965 Evaluate side-chains 56 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 90 optimal weight: 0.0980 chunk 205 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 117 optimal weight: 40.0000 chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.063141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.044015 restraints weight = 119587.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045310 restraints weight = 74037.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.046127 restraints weight = 55659.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046634 restraints weight = 46792.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.046953 restraints weight = 42207.696| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17374 Z= 0.176 Angle : 0.613 7.369 23691 Z= 0.313 Chirality : 0.044 0.178 2691 Planarity : 0.005 0.046 3032 Dihedral : 5.160 54.223 2427 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.42 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.18), residues: 2157 helix: 1.40 (0.54), residues: 78 sheet: 0.73 (0.17), residues: 963 loop : -0.82 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 107 TYR 0.015 0.001 TYR M 98 PHE 0.014 0.002 PHE L 99 TRP 0.009 0.001 TRP L 36 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00392 (17365) covalent geometry : angle 0.61327 (23673) SS BOND : bond 0.00411 ( 9) SS BOND : angle 0.71158 ( 18) hydrogen bonds : bond 0.03914 ( 590) hydrogen bonds : angle 5.88624 ( 1773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9403 (mmmt) cc_final: 0.9132 (tptp) REVERT: B 345 MET cc_start: 0.8898 (ppp) cc_final: 0.8419 (ppp) REVERT: D 31 ASN cc_start: 0.8811 (t0) cc_final: 0.8417 (t0) REVERT: D 214 ASN cc_start: 0.8914 (m-40) cc_final: 0.8698 (m-40) REVERT: H 31 ASN cc_start: 0.8697 (t0) cc_final: 0.8346 (t0) REVERT: H 73 ILE cc_start: 0.9156 (tp) cc_final: 0.8883 (pt) REVERT: M 31 ASN cc_start: 0.8868 (t0) cc_final: 0.8399 (t0) REVERT: M 214 ASN cc_start: 0.8798 (m-40) cc_final: 0.8590 (m-40) REVERT: N 137 LEU cc_start: 0.8870 (mm) cc_final: 0.8605 (mm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1120 time to fit residues: 14.8952 Evaluate side-chains 58 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 204 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.042359 restraints weight = 121546.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.043551 restraints weight = 77819.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.044312 restraints weight = 59537.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044759 restraints weight = 50466.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.044938 restraints weight = 45791.075| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17374 Z= 0.264 Angle : 0.716 8.576 23691 Z= 0.369 Chirality : 0.046 0.224 2691 Planarity : 0.005 0.046 3032 Dihedral : 5.792 53.023 2427 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.56 % Favored : 92.30 % Rotamer: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.18), residues: 2157 helix: 0.86 (0.54), residues: 78 sheet: 0.24 (0.17), residues: 963 loop : -1.04 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 25 TYR 0.023 0.002 TYR M 107 PHE 0.017 0.002 PHE E 99 TRP 0.009 0.002 TRP E 36 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00577 (17365) covalent geometry : angle 0.71516 (23673) SS BOND : bond 0.00584 ( 9) SS BOND : angle 1.07329 ( 18) hydrogen bonds : bond 0.03957 ( 590) hydrogen bonds : angle 6.25942 ( 1773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9382 (mmmt) cc_final: 0.8905 (tmtt) REVERT: B 178 LYS cc_start: 0.9396 (mmmt) cc_final: 0.8926 (tmtt) REVERT: B 345 MET cc_start: 0.8866 (ppp) cc_final: 0.8434 (ppp) REVERT: C 178 LYS cc_start: 0.9484 (tppt) cc_final: 0.9126 (tptp) REVERT: D 31 ASN cc_start: 0.8862 (t0) cc_final: 0.8492 (t0) REVERT: D 214 ASN cc_start: 0.8649 (m-40) cc_final: 0.8362 (m-40) REVERT: E 5 MET cc_start: 0.7638 (tpp) cc_final: 0.7196 (tpp) REVERT: E 137 LEU cc_start: 0.8924 (mm) cc_final: 0.8586 (mm) REVERT: H 31 ASN cc_start: 0.8811 (t0) cc_final: 0.8462 (t0) REVERT: H 214 ASN cc_start: 0.8973 (m-40) cc_final: 0.8734 (m-40) REVERT: M 31 ASN cc_start: 0.9027 (t0) cc_final: 0.8732 (t0) REVERT: M 214 ASN cc_start: 0.8751 (m-40) cc_final: 0.8544 (m-40) REVERT: N 137 LEU cc_start: 0.8841 (mm) cc_final: 0.8545 (mm) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.1108 time to fit residues: 11.1675 Evaluate side-chains 52 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 151 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 103 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN E 7 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.063453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044749 restraints weight = 120508.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046030 restraints weight = 76005.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046811 restraints weight = 57352.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047346 restraints weight = 48526.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047654 restraints weight = 43584.355| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17374 Z= 0.124 Angle : 0.596 8.301 23691 Z= 0.299 Chirality : 0.044 0.170 2691 Planarity : 0.004 0.047 3032 Dihedral : 5.114 48.437 2427 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.18), residues: 2157 helix: 0.89 (0.53), residues: 78 sheet: 0.46 (0.17), residues: 957 loop : -1.06 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 25 TYR 0.014 0.001 TYR M 98 PHE 0.019 0.001 PHE H 71 TRP 0.009 0.001 TRP N 36 HIS 0.002 0.001 HIS C 211 Details of bonding type rmsd covalent geometry : bond 0.00281 (17365) covalent geometry : angle 0.59553 (23673) SS BOND : bond 0.00773 ( 9) SS BOND : angle 0.64320 ( 18) hydrogen bonds : bond 0.03090 ( 590) hydrogen bonds : angle 5.59034 ( 1773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9391 (mmmt) cc_final: 0.8910 (tmtt) REVERT: A 345 MET cc_start: 0.8726 (ppp) cc_final: 0.8382 (ppp) REVERT: B 178 LYS cc_start: 0.9428 (mmmt) cc_final: 0.8980 (tmtt) REVERT: B 345 MET cc_start: 0.8645 (ppp) cc_final: 0.8260 (ppp) REVERT: C 178 LYS cc_start: 0.9472 (tppt) cc_final: 0.9228 (tmtt) REVERT: D 31 ASN cc_start: 0.8745 (t0) cc_final: 0.8457 (t0) REVERT: D 214 ASN cc_start: 0.8881 (m-40) cc_final: 0.8657 (m-40) REVERT: E 5 MET cc_start: 0.7660 (tpp) cc_final: 0.7454 (tpp) REVERT: E 137 LEU cc_start: 0.8942 (mm) cc_final: 0.8497 (mm) REVERT: H 31 ASN cc_start: 0.8575 (t0) cc_final: 0.8313 (t0) REVERT: H 73 ILE cc_start: 0.9217 (tp) cc_final: 0.8937 (mm) REVERT: H 214 ASN cc_start: 0.8976 (m-40) cc_final: 0.8692 (m-40) REVERT: M 31 ASN cc_start: 0.8807 (t0) cc_final: 0.8388 (t0) REVERT: M 214 ASN cc_start: 0.8720 (m-40) cc_final: 0.8510 (m-40) REVERT: N 94 TYR cc_start: 0.8341 (m-80) cc_final: 0.7844 (m-80) REVERT: N 137 LEU cc_start: 0.8833 (mm) cc_final: 0.8367 (mm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1042 time to fit residues: 13.4458 Evaluate side-chains 54 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 141 optimal weight: 6.9990 chunk 211 optimal weight: 20.0000 chunk 208 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 0.0030 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.062252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.043409 restraints weight = 116992.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044690 restraints weight = 72734.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045479 restraints weight = 54571.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046002 restraints weight = 45990.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046204 restraints weight = 41248.845| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17374 Z= 0.155 Angle : 0.614 8.264 23691 Z= 0.309 Chirality : 0.044 0.184 2691 Planarity : 0.004 0.045 3032 Dihedral : 5.068 53.082 2427 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.72 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.18), residues: 2157 helix: 0.92 (0.55), residues: 78 sheet: 0.39 (0.16), residues: 957 loop : -1.10 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 19 TYR 0.018 0.001 TYR M 107 PHE 0.013 0.002 PHE B 342 TRP 0.007 0.001 TRP E 36 HIS 0.003 0.001 HIS C 211 Details of bonding type rmsd covalent geometry : bond 0.00347 (17365) covalent geometry : angle 0.61405 (23673) SS BOND : bond 0.00482 ( 9) SS BOND : angle 0.63032 ( 18) hydrogen bonds : bond 0.03082 ( 590) hydrogen bonds : angle 5.55426 ( 1773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9392 (mmmt) cc_final: 0.8871 (tmtt) REVERT: B 178 LYS cc_start: 0.9395 (mmmt) cc_final: 0.8973 (tmtt) REVERT: B 345 MET cc_start: 0.8792 (ppp) cc_final: 0.8282 (ppp) REVERT: C 178 LYS cc_start: 0.9491 (tppt) cc_final: 0.9253 (tmtt) REVERT: D 31 ASN cc_start: 0.8809 (t0) cc_final: 0.8500 (t0) REVERT: D 214 ASN cc_start: 0.8899 (m-40) cc_final: 0.8669 (m-40) REVERT: H 31 ASN cc_start: 0.8701 (t0) cc_final: 0.8410 (t0) REVERT: H 214 ASN cc_start: 0.8990 (m-40) cc_final: 0.8696 (m-40) REVERT: M 31 ASN cc_start: 0.8978 (t0) cc_final: 0.8533 (t0) REVERT: M 214 ASN cc_start: 0.8706 (m-40) cc_final: 0.8434 (m-40) REVERT: N 94 TYR cc_start: 0.8276 (m-80) cc_final: 0.7691 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1138 time to fit residues: 12.4549 Evaluate side-chains 54 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 215 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 199 optimal weight: 0.0000 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 ASN ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.059329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.040750 restraints weight = 120452.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.041904 restraints weight = 76852.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.042638 restraints weight = 58784.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.043087 restraints weight = 49859.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.043335 restraints weight = 45212.274| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 17374 Z= 0.346 Angle : 0.805 9.681 23691 Z= 0.415 Chirality : 0.048 0.258 2691 Planarity : 0.006 0.066 3032 Dihedral : 6.197 55.593 2427 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.39 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.18), residues: 2157 helix: 0.20 (0.55), residues: 78 sheet: -0.22 (0.16), residues: 999 loop : -1.36 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 19 TYR 0.027 0.003 TYR D 107 PHE 0.022 0.003 PHE B 342 TRP 0.011 0.003 TRP E 36 HIS 0.006 0.002 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00752 (17365) covalent geometry : angle 0.80482 (23673) SS BOND : bond 0.00683 ( 9) SS BOND : angle 0.95043 ( 18) hydrogen bonds : bond 0.04399 ( 590) hydrogen bonds : angle 6.58588 ( 1773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9381 (mmmt) cc_final: 0.8834 (tmtt) REVERT: A 345 MET cc_start: 0.8781 (ppp) cc_final: 0.8400 (ppp) REVERT: B 345 MET cc_start: 0.8880 (ppp) cc_final: 0.8491 (ppp) REVERT: D 31 ASN cc_start: 0.8899 (t0) cc_final: 0.8618 (t0) REVERT: E 137 LEU cc_start: 0.8935 (tt) cc_final: 0.8451 (mm) REVERT: H 31 ASN cc_start: 0.8868 (t0) cc_final: 0.8579 (t0) REVERT: H 214 ASN cc_start: 0.8758 (m-40) cc_final: 0.8544 (m-40) REVERT: L 137 LEU cc_start: 0.8903 (tt) cc_final: 0.8390 (mm) REVERT: M 31 ASN cc_start: 0.9051 (t0) cc_final: 0.8761 (t0) REVERT: N 137 LEU cc_start: 0.8891 (tt) cc_final: 0.8382 (mm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1157 time to fit residues: 10.4193 Evaluate side-chains 35 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 13 optimal weight: 0.1980 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 7 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.062162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.043401 restraints weight = 117167.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044688 restraints weight = 72341.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045499 restraints weight = 54190.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046026 restraints weight = 45463.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.046352 restraints weight = 40774.707| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17374 Z= 0.123 Angle : 0.626 8.013 23691 Z= 0.312 Chirality : 0.045 0.164 2691 Planarity : 0.004 0.047 3032 Dihedral : 5.165 40.875 2427 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.18), residues: 2157 helix: 0.51 (0.55), residues: 78 sheet: 0.13 (0.17), residues: 957 loop : -1.34 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 19 TYR 0.013 0.001 TYR M 98 PHE 0.010 0.001 PHE B 174 TRP 0.009 0.001 TRP H 39 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00285 (17365) covalent geometry : angle 0.62624 (23673) SS BOND : bond 0.00374 ( 9) SS BOND : angle 0.71822 ( 18) hydrogen bonds : bond 0.03012 ( 590) hydrogen bonds : angle 5.70382 ( 1773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9424 (mmmt) cc_final: 0.8911 (tmtt) REVERT: A 345 MET cc_start: 0.8661 (ppp) cc_final: 0.8348 (ppp) REVERT: B 345 MET cc_start: 0.8650 (ppp) cc_final: 0.8356 (ppp) REVERT: D 31 ASN cc_start: 0.8733 (t0) cc_final: 0.8504 (t0) REVERT: D 214 ASN cc_start: 0.8966 (m-40) cc_final: 0.8693 (m-40) REVERT: E 137 LEU cc_start: 0.8878 (tt) cc_final: 0.8380 (mm) REVERT: H 31 ASN cc_start: 0.8650 (t0) cc_final: 0.8393 (t0) REVERT: H 214 ASN cc_start: 0.9001 (m-40) cc_final: 0.8681 (m-40) REVERT: L 137 LEU cc_start: 0.8854 (tt) cc_final: 0.8387 (mm) REVERT: M 31 ASN cc_start: 0.8893 (t0) cc_final: 0.8457 (t0) REVERT: N 137 LEU cc_start: 0.8912 (tt) cc_final: 0.8401 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1046 time to fit residues: 11.3956 Evaluate side-chains 46 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 193 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 203 optimal weight: 0.0770 chunk 65 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 67 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.062169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.043458 restraints weight = 117151.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044740 restraints weight = 72591.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045539 restraints weight = 54359.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046044 restraints weight = 45647.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046366 restraints weight = 40993.833| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17374 Z= 0.131 Angle : 0.598 7.439 23691 Z= 0.299 Chirality : 0.044 0.170 2691 Planarity : 0.004 0.044 3032 Dihedral : 4.903 34.863 2427 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.18), residues: 2157 helix: 0.65 (0.57), residues: 78 sheet: 0.21 (0.16), residues: 957 loop : -1.30 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 19 TYR 0.014 0.001 TYR D 107 PHE 0.011 0.001 PHE C 342 TRP 0.012 0.001 TRP E 36 HIS 0.003 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00301 (17365) covalent geometry : angle 0.59814 (23673) SS BOND : bond 0.00339 ( 9) SS BOND : angle 0.67327 ( 18) hydrogen bonds : bond 0.02873 ( 590) hydrogen bonds : angle 5.46250 ( 1773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9414 (mmmt) cc_final: 0.8912 (tmtt) REVERT: A 209 TYR cc_start: 0.7657 (m-80) cc_final: 0.7279 (m-80) REVERT: A 345 MET cc_start: 0.8691 (ppp) cc_final: 0.8474 (ppp) REVERT: D 31 ASN cc_start: 0.8843 (t0) cc_final: 0.8569 (t0) REVERT: D 214 ASN cc_start: 0.8963 (m-40) cc_final: 0.8686 (m-40) REVERT: E 137 LEU cc_start: 0.8923 (tt) cc_final: 0.8347 (mp) REVERT: H 31 ASN cc_start: 0.8772 (t0) cc_final: 0.8492 (t0) REVERT: H 214 ASN cc_start: 0.8951 (m-40) cc_final: 0.8612 (m-40) REVERT: L 137 LEU cc_start: 0.8904 (tt) cc_final: 0.8442 (mp) REVERT: M 31 ASN cc_start: 0.8907 (t0) cc_final: 0.8615 (t0) REVERT: M 214 ASN cc_start: 0.8899 (m-40) cc_final: 0.8579 (m-40) REVERT: N 137 LEU cc_start: 0.8925 (tt) cc_final: 0.8412 (mm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0943 time to fit residues: 9.8742 Evaluate side-chains 47 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 68 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 220 HIS C 199 HIS ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.061654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.042962 restraints weight = 117489.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.044218 restraints weight = 72908.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.044995 restraints weight = 54803.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045508 restraints weight = 46185.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045782 restraints weight = 41496.453| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17374 Z= 0.161 Angle : 0.616 7.422 23691 Z= 0.311 Chirality : 0.044 0.181 2691 Planarity : 0.004 0.042 3032 Dihedral : 5.007 34.588 2427 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.18), residues: 2157 helix: 0.53 (0.56), residues: 78 sheet: 0.16 (0.17), residues: 963 loop : -1.32 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 19 TYR 0.016 0.001 TYR D 107 PHE 0.027 0.002 PHE N 99 TRP 0.008 0.001 TRP E 36 HIS 0.004 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00361 (17365) covalent geometry : angle 0.61598 (23673) SS BOND : bond 0.00378 ( 9) SS BOND : angle 0.76243 ( 18) hydrogen bonds : bond 0.03052 ( 590) hydrogen bonds : angle 5.54736 ( 1773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9413 (mmmt) cc_final: 0.8893 (tmtt) REVERT: A 345 MET cc_start: 0.8728 (ppp) cc_final: 0.8488 (ppp) REVERT: B 209 TYR cc_start: 0.6591 (m-10) cc_final: 0.6384 (m-10) REVERT: D 31 ASN cc_start: 0.8878 (t0) cc_final: 0.8610 (t0) REVERT: D 214 ASN cc_start: 0.8994 (m-40) cc_final: 0.8719 (m-40) REVERT: E 5 MET cc_start: 0.7214 (tpt) cc_final: 0.6767 (tpp) REVERT: E 137 LEU cc_start: 0.8876 (tt) cc_final: 0.8262 (mp) REVERT: H 31 ASN cc_start: 0.8826 (t0) cc_final: 0.8514 (t0) REVERT: H 214 ASN cc_start: 0.8760 (m-40) cc_final: 0.8555 (m-40) REVERT: L 137 LEU cc_start: 0.8911 (tt) cc_final: 0.8445 (mp) REVERT: M 31 ASN cc_start: 0.8992 (t0) cc_final: 0.8684 (t0) REVERT: M 214 ASN cc_start: 0.8928 (m-40) cc_final: 0.8570 (m-40) REVERT: N 137 LEU cc_start: 0.8938 (tt) cc_final: 0.8379 (mp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1021 time to fit residues: 10.5273 Evaluate side-chains 44 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 81 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 177 optimal weight: 0.0470 chunk 135 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 ASN ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.059750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.041498 restraints weight = 121501.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.042630 restraints weight = 78075.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.043320 restraints weight = 59949.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.043777 restraints weight = 51303.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.044066 restraints weight = 46502.620| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17374 Z= 0.286 Angle : 0.731 7.565 23691 Z= 0.377 Chirality : 0.047 0.223 2691 Planarity : 0.005 0.065 3032 Dihedral : 5.783 35.598 2427 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.18), residues: 2157 helix: -0.06 (0.55), residues: 78 sheet: -0.24 (0.17), residues: 972 loop : -1.40 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 19 TYR 0.026 0.002 TYR M 107 PHE 0.017 0.002 PHE A 342 TRP 0.010 0.002 TRP E 36 HIS 0.010 0.002 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00625 (17365) covalent geometry : angle 0.73131 (23673) SS BOND : bond 0.00537 ( 9) SS BOND : angle 0.92151 ( 18) hydrogen bonds : bond 0.03932 ( 590) hydrogen bonds : angle 6.29562 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.58 seconds wall clock time: 44 minutes 20.95 seconds (2660.95 seconds total)