Starting phenix.real_space_refine on Sun Jun 15 09:22:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8goo_34178/06_2025/8goo_34178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8goo_34178/06_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_34178/06_2025/8goo_34178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8goo_34178/06_2025/8goo_34178.map" model { file = "/net/cci-nas-00/data/ceres_data/8goo_34178/06_2025/8goo_34178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8goo_34178/06_2025/8goo_34178.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ASN:plan1': 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, 'HIS:plan': 1, 'ASP:plan': 3} 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: {'GLU:plan': 1, 'ASN:plan1': 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, 'HIS:plan': 1, 'ASP:plan': 3} 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: {'GLU:plan': 1, 'ASN:plan1': 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, 'HIS:plan': 1, 'ASP:plan': 3} 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: 10.64, per 1000 atoms: 0.63 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: 4.07 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.44 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: 6.36 Time building geometry restraints manager: 4.83 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: 3.340 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: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.640 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.430 ------------------------------------------------------------------------------- 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 : 10.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (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 TRP 0.004 0.001 TRP E 36 HIS 0.002 0.000 HIS A 346 PHE 0.009 0.001 PHE M 30 TYR 0.007 0.001 TYR N 174 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.25690 ( 590) hydrogen bonds : angle 9.34508 ( 1773) SS BOND : bond 0.00113 ( 9) SS BOND : angle 0.34473 ( 18) covalent geometry : bond 0.00446 (17365) covalent geometry : angle 0.65953 (23673) *********************** 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 : 1.941 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: 0.2911 time to fit residues: 49.3697 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 : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 2.9990 chunk 165 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 125 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 = 0.3499 r_free = 0.3499 target = 0.064819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045644 restraints weight = 116498.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046946 restraints weight = 72801.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.047766 restraints weight = 55081.271| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17374 Z= 0.183 Angle : 0.621 7.116 23691 Z= 0.320 Chirality : 0.044 0.174 2691 Planarity : 0.004 0.046 3032 Dihedral : 4.947 47.446 2427 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.91 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 2157 helix: 2.07 (0.58), residues: 78 sheet: 1.05 (0.17), residues: 951 loop : -0.69 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 36 HIS 0.003 0.001 HIS C 199 PHE 0.010 0.002 PHE B 145 TYR 0.015 0.002 TYR M 98 ARG 0.005 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 590) hydrogen bonds : angle 6.33328 ( 1773) SS BOND : bond 0.00542 ( 9) SS BOND : angle 1.01140 ( 18) covalent geometry : bond 0.00400 (17365) covalent geometry : angle 0.62060 (23673) *********************** 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 85 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9192 (mm) cc_final: 0.8795 (mm) REVERT: A 345 MET cc_start: 0.8564 (ppp) cc_final: 0.8278 (ppp) REVERT: C 141 LEU cc_start: 0.9303 (pt) cc_final: 0.9068 (mt) REVERT: D 31 ASN cc_start: 0.8958 (t0) cc_final: 0.8458 (t0) REVERT: H 31 ASN cc_start: 0.8806 (t0) cc_final: 0.8369 (t0) REVERT: H 73 ILE cc_start: 0.9088 (tp) cc_final: 0.8789 (pt) REVERT: M 31 ASN cc_start: 0.9033 (t0) cc_final: 0.8495 (t0) REVERT: M 214 ASN cc_start: 0.8808 (m-40) cc_final: 0.8594 (m-40) REVERT: N 137 LEU cc_start: 0.9002 (mm) cc_final: 0.8749 (mm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2320 time to fit residues: 34.4301 Evaluate side-chains 59 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 121 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** 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 125 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** N 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.041629 restraints weight = 118384.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.042826 restraints weight = 75036.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.043565 restraints weight = 57120.747| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17374 Z= 0.294 Angle : 0.772 9.979 23691 Z= 0.400 Chirality : 0.048 0.220 2691 Planarity : 0.006 0.051 3032 Dihedral : 6.167 58.064 2427 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2157 helix: 1.08 (0.56), residues: 78 sheet: 0.14 (0.17), residues: 999 loop : -0.94 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 36 HIS 0.007 0.002 HIS A 114 PHE 0.024 0.003 PHE L 99 TYR 0.021 0.002 TYR L 56 ARG 0.006 0.001 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 590) hydrogen bonds : angle 6.63197 ( 1773) SS BOND : bond 0.00687 ( 9) SS BOND : angle 1.28695 ( 18) covalent geometry : bond 0.00640 (17365) covalent geometry : angle 0.77128 (23673) *********************** 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 61 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9361 (mmmt) cc_final: 0.8907 (tmtt) REVERT: B 345 MET cc_start: 0.8966 (ppp) cc_final: 0.8527 (ppp) REVERT: D 31 ASN cc_start: 0.8841 (t0) cc_final: 0.8457 (t0) REVERT: H 31 ASN cc_start: 0.8737 (t0) cc_final: 0.8433 (t0) REVERT: M 31 ASN cc_start: 0.8940 (t0) cc_final: 0.8617 (t0) REVERT: M 214 ASN cc_start: 0.8772 (m-40) cc_final: 0.8570 (m-40) REVERT: N 137 LEU cc_start: 0.8836 (mm) cc_final: 0.8547 (mm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2660 time to fit residues: 27.6697 Evaluate side-chains 43 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.063703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.044639 restraints weight = 115140.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046001 restraints weight = 70190.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046863 restraints weight = 52164.705| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3459 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= 0.112 Angle : 0.595 8.095 23691 Z= 0.297 Chirality : 0.045 0.165 2691 Planarity : 0.004 0.048 3032 Dihedral : 5.086 59.042 2427 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2157 helix: 1.30 (0.53), residues: 78 sheet: 0.54 (0.17), residues: 963 loop : -0.97 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 36 HIS 0.003 0.001 HIS C 220 PHE 0.011 0.001 PHE C 174 TYR 0.012 0.001 TYR M 107 ARG 0.004 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 590) hydrogen bonds : angle 5.62306 ( 1773) SS BOND : bond 0.00394 ( 9) SS BOND : angle 0.66301 ( 18) covalent geometry : bond 0.00254 (17365) covalent geometry : angle 0.59496 (23673) *********************** 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 92 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9381 (mmmt) cc_final: 0.8884 (tmtt) REVERT: B 345 MET cc_start: 0.8867 (ppp) cc_final: 0.8439 (ppp) REVERT: D 31 ASN cc_start: 0.8792 (t0) cc_final: 0.8513 (t0) REVERT: E 137 LEU cc_start: 0.8944 (mm) cc_final: 0.8514 (mm) REVERT: H 31 ASN cc_start: 0.8629 (t0) cc_final: 0.8310 (t0) REVERT: H 214 ASN cc_start: 0.9034 (m-40) cc_final: 0.8787 (m-40) REVERT: M 31 ASN cc_start: 0.8845 (t0) cc_final: 0.8469 (t0) REVERT: M 214 ASN cc_start: 0.8884 (m-40) cc_final: 0.8670 (m-40) REVERT: N 94 TYR cc_start: 0.8365 (m-80) cc_final: 0.7877 (m-80) REVERT: N 137 LEU cc_start: 0.8829 (mm) cc_final: 0.8408 (mm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2508 time to fit residues: 38.8450 Evaluate side-chains 61 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 89 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 211 optimal weight: 20.0000 chunk 176 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 167 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.063635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044792 restraints weight = 116003.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.046114 restraints weight = 71652.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046929 restraints weight = 53595.034| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17374 Z= 0.108 Angle : 0.575 7.800 23691 Z= 0.286 Chirality : 0.044 0.168 2691 Planarity : 0.004 0.046 3032 Dihedral : 4.842 55.384 2427 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.42 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2157 helix: 1.41 (0.54), residues: 78 sheet: 0.63 (0.16), residues: 957 loop : -0.95 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 36 HIS 0.004 0.001 HIS C 199 PHE 0.011 0.001 PHE C 174 TYR 0.012 0.001 TYR M 98 ARG 0.003 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.02887 ( 590) hydrogen bonds : angle 5.31865 ( 1773) SS BOND : bond 0.00343 ( 9) SS BOND : angle 0.55000 ( 18) covalent geometry : bond 0.00248 (17365) covalent geometry : angle 0.57472 (23673) *********************** 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 84 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9370 (mmmt) cc_final: 0.8867 (tmtt) REVERT: A 345 MET cc_start: 0.8683 (ppp) cc_final: 0.8346 (ppp) REVERT: B 345 MET cc_start: 0.8593 (ppp) cc_final: 0.8078 (ppp) REVERT: D 31 ASN cc_start: 0.8753 (t0) cc_final: 0.8491 (t0) REVERT: E 5 MET cc_start: 0.7465 (tpp) cc_final: 0.6920 (tpp) REVERT: E 94 TYR cc_start: 0.8516 (m-80) cc_final: 0.8007 (m-80) REVERT: H 31 ASN cc_start: 0.8577 (t0) cc_final: 0.8285 (t0) REVERT: H 214 ASN cc_start: 0.9057 (m-40) cc_final: 0.8810 (m-40) REVERT: M 31 ASN cc_start: 0.8900 (t0) cc_final: 0.8447 (t0) REVERT: M 214 ASN cc_start: 0.8883 (m-40) cc_final: 0.8678 (m-40) REVERT: N 94 TYR cc_start: 0.8379 (m-80) cc_final: 0.7777 (m-80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2411 time to fit residues: 34.7013 Evaluate side-chains 61 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 167 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 180 optimal weight: 0.5980 chunk 141 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.063249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.044307 restraints weight = 117244.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045632 restraints weight = 72225.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046481 restraints weight = 53925.535| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17374 Z= 0.126 Angle : 0.588 8.742 23691 Z= 0.292 Chirality : 0.044 0.179 2691 Planarity : 0.004 0.045 3032 Dihedral : 4.829 46.992 2427 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2157 helix: 1.37 (0.56), residues: 78 sheet: 0.61 (0.16), residues: 957 loop : -0.96 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.003 0.001 HIS C 199 PHE 0.010 0.001 PHE B 342 TYR 0.013 0.001 TYR M 98 ARG 0.003 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.02859 ( 590) hydrogen bonds : angle 5.19041 ( 1773) SS BOND : bond 0.00345 ( 9) SS BOND : angle 0.54806 ( 18) covalent geometry : bond 0.00289 (17365) covalent geometry : angle 0.58805 (23673) *********************** 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 71 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9373 (mmmt) cc_final: 0.8835 (tmtt) REVERT: A 209 TYR cc_start: 0.7427 (m-80) cc_final: 0.7196 (m-10) REVERT: B 345 MET cc_start: 0.8830 (ppp) cc_final: 0.8355 (ppp) REVERT: D 31 ASN cc_start: 0.8872 (t0) cc_final: 0.8619 (t0) REVERT: E 5 MET cc_start: 0.7530 (tpp) cc_final: 0.7287 (tpp) REVERT: E 137 LEU cc_start: 0.8879 (tt) cc_final: 0.8389 (mm) REVERT: H 31 ASN cc_start: 0.8697 (t0) cc_final: 0.8427 (t0) REVERT: H 73 ILE cc_start: 0.9200 (tp) cc_final: 0.8800 (mm) REVERT: H 214 ASN cc_start: 0.8960 (m-40) cc_final: 0.8678 (m-40) REVERT: L 137 LEU cc_start: 0.8898 (tt) cc_final: 0.8455 (mm) REVERT: M 31 ASN cc_start: 0.9017 (t0) cc_final: 0.8546 (t0) REVERT: N 94 TYR cc_start: 0.8320 (m-80) cc_final: 0.7571 (m-10) REVERT: N 137 LEU cc_start: 0.8938 (tt) cc_final: 0.8424 (mm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2505 time to fit residues: 29.7975 Evaluate side-chains 59 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 104 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 82 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.062753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.043898 restraints weight = 117396.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.045205 restraints weight = 72576.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046020 restraints weight = 54289.621| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17374 Z= 0.143 Angle : 0.594 7.630 23691 Z= 0.298 Chirality : 0.044 0.181 2691 Planarity : 0.004 0.045 3032 Dihedral : 4.863 41.003 2427 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2157 helix: 1.41 (0.57), residues: 78 sheet: 0.54 (0.16), residues: 957 loop : -1.01 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 36 HIS 0.003 0.001 HIS C 114 PHE 0.022 0.001 PHE H 71 TYR 0.015 0.001 TYR M 107 ARG 0.007 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.02965 ( 590) hydrogen bonds : angle 5.19574 ( 1773) SS BOND : bond 0.00357 ( 9) SS BOND : angle 0.56576 ( 18) covalent geometry : bond 0.00322 (17365) covalent geometry : angle 0.59416 (23673) *********************** 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 67 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9378 (mmmt) cc_final: 0.8861 (tmtt) REVERT: A 209 TYR cc_start: 0.7603 (m-80) cc_final: 0.7185 (m-10) REVERT: A 345 MET cc_start: 0.8543 (ppp) cc_final: 0.8336 (ppp) REVERT: B 178 LYS cc_start: 0.9392 (mmmt) cc_final: 0.8964 (tmtt) REVERT: B 345 MET cc_start: 0.8869 (ppp) cc_final: 0.8362 (ppp) REVERT: D 31 ASN cc_start: 0.8855 (t0) cc_final: 0.8505 (t0) REVERT: E 5 MET cc_start: 0.7823 (tpp) cc_final: 0.7622 (tpp) REVERT: E 137 LEU cc_start: 0.8882 (tt) cc_final: 0.8339 (mm) REVERT: H 31 ASN cc_start: 0.8741 (t0) cc_final: 0.8424 (t0) REVERT: H 73 ILE cc_start: 0.9179 (tp) cc_final: 0.8970 (pt) REVERT: H 214 ASN cc_start: 0.9007 (m-40) cc_final: 0.8746 (m-40) REVERT: L 137 LEU cc_start: 0.8908 (tt) cc_final: 0.8404 (mm) REVERT: M 31 ASN cc_start: 0.9020 (t0) cc_final: 0.8522 (t0) REVERT: N 137 LEU cc_start: 0.8922 (tt) cc_final: 0.8368 (mm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2515 time to fit residues: 28.7773 Evaluate side-chains 57 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 179 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.060878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.042194 restraints weight = 118461.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.043410 restraints weight = 74914.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.044147 restraints weight = 56830.551| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17374 Z= 0.240 Angle : 0.686 7.640 23691 Z= 0.351 Chirality : 0.045 0.211 2691 Planarity : 0.005 0.048 3032 Dihedral : 5.421 46.118 2427 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.88 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2157 helix: 0.92 (0.55), residues: 78 sheet: 0.12 (0.16), residues: 996 loop : -1.17 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 106 HIS 0.005 0.001 HIS B 220 PHE 0.018 0.002 PHE H 71 TYR 0.026 0.002 TYR H 107 ARG 0.005 0.001 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 590) hydrogen bonds : angle 5.72676 ( 1773) SS BOND : bond 0.00681 ( 9) SS BOND : angle 0.82925 ( 18) covalent geometry : bond 0.00525 (17365) covalent geometry : angle 0.68618 (23673) *********************** 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 57 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9401 (mmmt) cc_final: 0.8888 (tmtt) REVERT: A 209 TYR cc_start: 0.7946 (m-80) cc_final: 0.7325 (m-80) REVERT: A 345 MET cc_start: 0.8791 (ppp) cc_final: 0.8486 (ppp) REVERT: B 345 MET cc_start: 0.8844 (ppp) cc_final: 0.8338 (ppp) REVERT: D 31 ASN cc_start: 0.8876 (t0) cc_final: 0.8585 (t0) REVERT: E 137 LEU cc_start: 0.8930 (tt) cc_final: 0.8412 (mm) REVERT: H 31 ASN cc_start: 0.8863 (t0) cc_final: 0.8521 (t0) REVERT: H 214 ASN cc_start: 0.9025 (m-40) cc_final: 0.8730 (m-40) REVERT: L 137 LEU cc_start: 0.8976 (tt) cc_final: 0.8504 (mm) REVERT: M 31 ASN cc_start: 0.8999 (t0) cc_final: 0.8661 (t0) REVERT: M 214 ASN cc_start: 0.8883 (m-40) cc_final: 0.8576 (m-40) REVERT: N 137 LEU cc_start: 0.8989 (tt) cc_final: 0.8491 (mm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2508 time to fit residues: 24.7043 Evaluate side-chains 42 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 203 optimal weight: 0.0040 chunk 205 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.062284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.043456 restraints weight = 117365.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044758 restraints weight = 72591.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045580 restraints weight = 54406.894| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17374 Z= 0.137 Angle : 0.606 7.458 23691 Z= 0.303 Chirality : 0.044 0.175 2691 Planarity : 0.004 0.048 3032 Dihedral : 4.987 48.681 2427 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 2157 helix: 0.91 (0.55), residues: 78 sheet: 0.32 (0.16), residues: 957 loop : -1.18 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 36 HIS 0.003 0.001 HIS A 211 PHE 0.028 0.001 PHE M 71 TYR 0.013 0.001 TYR M 98 ARG 0.004 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 590) hydrogen bonds : angle 5.35249 ( 1773) SS BOND : bond 0.00373 ( 9) SS BOND : angle 0.73374 ( 18) covalent geometry : bond 0.00312 (17365) covalent geometry : angle 0.60606 (23673) *********************** 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 64 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9419 (mmmt) cc_final: 0.8912 (tmtt) REVERT: A 209 TYR cc_start: 0.7755 (m-80) cc_final: 0.7166 (m-80) REVERT: A 345 MET cc_start: 0.8634 (ppp) cc_final: 0.8367 (ppp) REVERT: B 209 TYR cc_start: 0.6595 (m-10) cc_final: 0.6311 (m-10) REVERT: B 345 MET cc_start: 0.8810 (ppp) cc_final: 0.8425 (ppp) REVERT: D 31 ASN cc_start: 0.8884 (t0) cc_final: 0.8643 (t0) REVERT: E 137 LEU cc_start: 0.8877 (tt) cc_final: 0.8357 (mm) REVERT: H 31 ASN cc_start: 0.8713 (t0) cc_final: 0.8445 (t0) REVERT: H 214 ASN cc_start: 0.8902 (m-40) cc_final: 0.8599 (m-40) REVERT: L 137 LEU cc_start: 0.8891 (tt) cc_final: 0.8417 (mm) REVERT: M 31 ASN cc_start: 0.8950 (t0) cc_final: 0.8621 (t0) REVERT: M 214 ASN cc_start: 0.8866 (m-40) cc_final: 0.8521 (m-40) REVERT: N 137 LEU cc_start: 0.8958 (tt) cc_final: 0.8482 (mm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2409 time to fit residues: 26.4644 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 : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 99 optimal weight: 4.9990 chunk 106 optimal weight: 0.2980 chunk 165 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 200 optimal weight: 0.0570 chunk 179 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3487 r_free = 0.3487 target = 0.064069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045750 restraints weight = 120393.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047036 restraints weight = 75856.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047855 restraints weight = 57147.896| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17374 Z= 0.098 Angle : 0.579 7.510 23691 Z= 0.284 Chirality : 0.044 0.153 2691 Planarity : 0.004 0.044 3032 Dihedral : 4.619 50.985 2427 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2157 helix: 1.09 (0.57), residues: 78 sheet: 0.53 (0.16), residues: 975 loop : -1.17 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 36 HIS 0.003 0.000 HIS C 346 PHE 0.013 0.001 PHE M 71 TYR 0.009 0.001 TYR H 98 ARG 0.004 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.02583 ( 590) hydrogen bonds : angle 4.92342 ( 1773) SS BOND : bond 0.00355 ( 9) SS BOND : angle 0.59739 ( 18) covalent geometry : bond 0.00231 (17365) covalent geometry : angle 0.57873 (23673) ********************** 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 72 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9399 (mmmt) cc_final: 0.8884 (tmtt) REVERT: B 209 TYR cc_start: 0.6208 (m-10) cc_final: 0.5968 (m-10) REVERT: B 345 MET cc_start: 0.8628 (ppp) cc_final: 0.8298 (ppp) REVERT: D 31 ASN cc_start: 0.8790 (t0) cc_final: 0.8466 (t0) REVERT: E 137 LEU cc_start: 0.8861 (tt) cc_final: 0.8327 (mm) REVERT: H 31 ASN cc_start: 0.8680 (t0) cc_final: 0.8307 (t0) REVERT: H 214 ASN cc_start: 0.8988 (m-40) cc_final: 0.8707 (m-40) REVERT: L 137 LEU cc_start: 0.8900 (tt) cc_final: 0.8454 (mp) REVERT: M 31 ASN cc_start: 0.8954 (t0) cc_final: 0.8546 (t0) REVERT: M 214 ASN cc_start: 0.9008 (m-40) cc_final: 0.8690 (m-40) REVERT: N 137 LEU cc_start: 0.8951 (tt) cc_final: 0.8470 (mm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2480 time to fit residues: 30.9032 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 : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 18 optimal weight: 0.0670 chunk 143 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.063184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.044558 restraints weight = 118065.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045849 restraints weight = 73316.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.046646 restraints weight = 55039.495| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4653 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= 0.114 Angle : 0.573 7.239 23691 Z= 0.283 Chirality : 0.044 0.171 2691 Planarity : 0.004 0.042 3032 Dihedral : 4.622 55.249 2427 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2157 helix: 1.09 (0.58), residues: 78 sheet: 0.50 (0.16), residues: 957 loop : -1.11 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 36 HIS 0.002 0.001 HIS D 38 PHE 0.012 0.001 PHE M 71 TYR 0.011 0.001 TYR H 107 ARG 0.003 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.02644 ( 590) hydrogen bonds : angle 4.91620 ( 1773) SS BOND : bond 0.00286 ( 9) SS BOND : angle 0.60340 ( 18) covalent geometry : bond 0.00263 (17365) covalent geometry : angle 0.57298 (23673) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4934.31 seconds wall clock time: 87 minutes 8.33 seconds (5228.33 seconds total)