Starting phenix.real_space_refine on Sun Dec 10 11:54:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/12_2023/8h2t_34443_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/12_2023/8h2t_34443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/12_2023/8h2t_34443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/12_2023/8h2t_34443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/12_2023/8h2t_34443_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h2t_34443/12_2023/8h2t_34443_updated.pdb" } resolution = 2.59 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= 1.000 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 Fe 9 7.16 5 S 87 5.16 5 C 9066 2.51 5 N 2568 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 101": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14370 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3537 Chain: "A" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1305 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 149} Chain: "D" Number of atoms: 3467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3537 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1305 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 149} Chain: "G" Number of atoms: 3467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 435, 3456 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3537 Chain: "H" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1305 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 149} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' FE': 1, 'FES': 1, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' FE': 1, 'FES': 1, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' FE': 1, 'FES': 1, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 681 SG CYS B 85 63.869 23.859 63.621 1.00 77.23 S ATOM 837 SG CYS B 106 64.771 24.572 60.097 1.00 86.23 S ATOM 5453 SG CYS D 85 92.651 68.268 63.635 1.00 82.70 S ATOM 5609 SG CYS D 106 91.640 68.795 60.069 1.00 84.01 S ATOM 10225 SG CYS G 85 39.814 71.048 63.604 1.00 79.87 S ATOM 10381 SG CYS G 106 39.938 69.893 60.076 1.00 85.39 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG B 230 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG B 230 " occ=0.51 residue: pdb=" N AARG D 230 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG D 230 " occ=0.51 residue: pdb=" N AARG G 230 " occ=0.46 ... (20 atoms not shown) pdb=" NH2BARG G 230 " occ=0.54 Time building chain proxies: 12.39, per 1000 atoms: 0.86 Number of scatterers: 14370 At special positions: 0 Unit cell: (121.55, 120.7, 95.2, 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) Fe 9 26.01 S 87 16.00 O 2640 8.00 N 2568 7.00 C 9066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES B 501 " pdb="FE1 FES B 501 " - pdb=" ND1 HIS B 87 " pdb="FE1 FES B 501 " - pdb=" ND1 HIS B 109 " pdb="FE2 FES B 501 " - pdb=" SG CYS B 106 " pdb="FE2 FES B 501 " - pdb=" SG CYS B 85 " pdb=" FES D 501 " pdb="FE1 FES D 501 " - pdb=" ND1 HIS D 109 " pdb="FE1 FES D 501 " - pdb=" ND1 HIS D 87 " pdb="FE2 FES D 501 " - pdb=" SG CYS D 106 " pdb="FE2 FES D 501 " - pdb=" SG CYS D 85 " pdb=" FES G 501 " pdb="FE1 FES G 501 " - pdb=" ND1 HIS G 87 " pdb="FE1 FES G 501 " - pdb=" ND1 HIS G 109 " pdb="FE2 FES G 501 " - pdb=" SG CYS G 106 " pdb="FE2 FES G 501 " - pdb=" SG CYS G 85 " Number of angles added : 9 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 24 sheets defined 33.2% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'B' and resid 8 through 14 removed outlier: 3.799A pdb=" N LEU B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.605A pdb=" N THR B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 37 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 173 through 182 Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.802A pdb=" N LEU B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 232 removed outlier: 4.582A pdb=" N GLU B 222 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER B 223 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N SER B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 252 Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 353 through 367 Processing helix chain 'B' and resid 372 through 389 removed outlier: 4.565A pdb=" N HIS B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.595A pdb=" N LYS B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 436 removed outlier: 4.513A pdb=" N THR B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.589A pdb=" N ALA A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 3.626A pdb=" N LEU A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.850A pdb=" N LEU D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 26 removed outlier: 3.585A pdb=" N THR D 26 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 37 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 125 through 128 Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.753A pdb=" N LEU D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 232 removed outlier: 4.743A pdb=" N GLU D 222 " --> pdb=" O MET D 218 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N SER D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 Proline residue: D 250 - end of helix Processing helix chain 'D' and resid 255 through 261 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 353 through 367 Processing helix chain 'D' and resid 372 through 389 removed outlier: 4.589A pdb=" N HIS D 389 " --> pdb=" O GLN D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 408 removed outlier: 3.559A pdb=" N LYS D 408 " --> pdb=" O SER D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 435 Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 27 through 33 removed outlier: 3.570A pdb=" N ALA E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 73 removed outlier: 3.598A pdb=" N LEU E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'G' and resid 8 through 14 removed outlier: 3.885A pdb=" N LEU G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 26 removed outlier: 3.533A pdb=" N THR G 26 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 125 through 128 Processing helix chain 'G' and resid 133 through 135 No H-bonds generated for 'chain 'G' and resid 133 through 135' Processing helix chain 'G' and resid 166 through 170 Processing helix chain 'G' and resid 173 through 182 Processing helix chain 'G' and resid 204 through 212 removed outlier: 3.815A pdb=" N LEU G 211 " --> pdb=" O PHE G 207 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN G 212 " --> pdb=" O VAL G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 232 removed outlier: 4.643A pdb=" N GLU G 222 " --> pdb=" O MET G 218 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER G 223 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N SER G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 Proline residue: G 250 - end of helix Processing helix chain 'G' and resid 255 through 261 Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 300 through 306 Processing helix chain 'G' and resid 353 through 367 Processing helix chain 'G' and resid 372 through 389 removed outlier: 4.646A pdb=" N HIS G 389 " --> pdb=" O GLN G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 408 removed outlier: 3.567A pdb=" N LYS G 408 " --> pdb=" O SER G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 435 Processing helix chain 'H' and resid 8 through 23 Processing helix chain 'H' and resid 27 through 33 removed outlier: 3.598A pdb=" N ALA H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 73 removed outlier: 3.641A pdb=" N LEU H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing sheet with id= A, first strand: chain 'B' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'B' and resid 97 through 99 removed outlier: 4.353A pdb=" N ASP B 57 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= D, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.844A pdb=" N GLY B 47 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 157 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR B 45 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 191 Processing sheet with id= F, first strand: chain 'B' and resid 196 through 200 removed outlier: 3.803A pdb=" N ARG B 338 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 340 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU B 342 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL B 331 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TRP B 344 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG B 329 " --> pdb=" O TRP B 344 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 327 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 312 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 56 through 60 removed outlier: 6.414A pdb=" N VAL A 42 " --> pdb=" O HIS A 57 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 59 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR A 40 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 39 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU A 148 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS A 131 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS A 144 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE A 129 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL A 146 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 127 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 148 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 125 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 94 through 99 removed outlier: 6.749A pdb=" N VAL A 106 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 98 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG A 104 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 19 through 21 Processing sheet with id= J, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.344A pdb=" N ASP D 57 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 103 through 105 Processing sheet with id= L, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.843A pdb=" N GLY D 47 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 157 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR D 45 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 189 through 191 Processing sheet with id= N, first strand: chain 'D' and resid 195 through 200 removed outlier: 3.868A pdb=" N ALA D 327 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 312 " --> pdb=" O THR D 273 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 56 through 60 removed outlier: 6.405A pdb=" N VAL E 42 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR E 59 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR E 40 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE E 39 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU E 148 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS E 131 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS E 144 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE E 129 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL E 146 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR E 127 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU E 148 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL E 125 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 94 through 99 removed outlier: 6.651A pdb=" N VAL E 106 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE E 98 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG E 104 " --> pdb=" O PHE E 98 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 19 through 21 Processing sheet with id= R, first strand: chain 'G' and resid 97 through 99 removed outlier: 4.361A pdb=" N ASP G 57 " --> pdb=" O ARG G 72 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 103 through 105 Processing sheet with id= T, first strand: chain 'G' and resid 148 through 151 removed outlier: 3.871A pdb=" N GLY G 47 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL G 157 " --> pdb=" O TYR G 45 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR G 45 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 189 through 191 Processing sheet with id= V, first strand: chain 'G' and resid 196 through 200 removed outlier: 3.778A pdb=" N ARG G 338 " --> pdb=" O SER G 335 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU G 340 " --> pdb=" O PRO G 333 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU G 342 " --> pdb=" O VAL G 331 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL G 331 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TRP G 344 " --> pdb=" O ARG G 329 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG G 329 " --> pdb=" O TRP G 344 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA G 327 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN G 312 " --> pdb=" O THR G 273 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 56 through 60 removed outlier: 6.394A pdb=" N VAL H 42 " --> pdb=" O HIS H 57 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR H 59 " --> pdb=" O TYR H 40 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR H 40 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 39 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU H 148 " --> pdb=" O PRO H 43 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS H 131 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS H 144 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE H 129 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL H 146 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR H 127 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU H 148 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL H 125 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 94 through 99 removed outlier: 6.689A pdb=" N VAL H 106 " --> pdb=" O GLU H 96 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE H 98 " --> pdb=" O ARG H 104 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ARG H 104 " --> pdb=" O PHE H 98 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1446 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: 4.74 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 6505 1.42 - 1.62: 8099 1.62 - 1.81: 137 1.81 - 2.01: 1 2.01 - 2.20: 12 Bond restraints: 14754 Sorted by residual: bond pdb=" N IAC B 502 " pdb=" C IAC B 502 " ideal model delta sigma weight residual 1.363 1.331 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" N IAC D 502 " pdb=" C IAC D 502 " ideal model delta sigma weight residual 1.363 1.331 0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C7 IAC B 502 " pdb=" C8 IAC B 502 " ideal model delta sigma weight residual 1.366 1.397 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" N IAC G 502 " pdb=" C IAC G 502 " ideal model delta sigma weight residual 1.363 1.332 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C7 IAC D 502 " pdb=" C8 IAC D 502 " ideal model delta sigma weight residual 1.366 1.396 -0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 14749 not shown) Histogram of bond angle deviations from ideal: 75.50 - 87.59: 6 87.59 - 99.68: 1 99.68 - 111.77: 6892 111.77 - 123.86: 12604 123.86 - 135.95: 489 Bond angle restraints: 19992 Sorted by residual: angle pdb=" CB MET D 215 " pdb=" CG MET D 215 " pdb=" SD MET D 215 " ideal model delta sigma weight residual 112.70 124.81 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" N ILE G 325 " pdb=" CA ILE G 325 " pdb=" C ILE G 325 " ideal model delta sigma weight residual 113.42 108.99 4.43 1.17e+00 7.31e-01 1.44e+01 angle pdb=" N ILE B 325 " pdb=" CA ILE B 325 " pdb=" C ILE B 325 " ideal model delta sigma weight residual 113.42 108.99 4.43 1.17e+00 7.31e-01 1.43e+01 angle pdb=" N ILE D 325 " pdb=" CA ILE D 325 " pdb=" C ILE D 325 " ideal model delta sigma weight residual 113.42 109.04 4.38 1.17e+00 7.31e-01 1.40e+01 angle pdb=" C HIS B 276 " pdb=" N PHE B 277 " pdb=" CA PHE B 277 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.38e+01 ... (remaining 19987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 7529 16.96 - 33.91: 892 33.91 - 50.87: 235 50.87 - 67.82: 57 67.82 - 84.78: 23 Dihedral angle restraints: 8736 sinusoidal: 3567 harmonic: 5169 Sorted by residual: dihedral pdb=" CA LEU E 90 " pdb=" C LEU E 90 " pdb=" N GLN E 91 " pdb=" CA GLN E 91 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LEU A 90 " pdb=" C LEU A 90 " pdb=" N GLN A 91 " pdb=" CA GLN A 91 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU H 90 " pdb=" C LEU H 90 " pdb=" N GLN H 91 " pdb=" CA GLN H 91 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 8733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1254 0.030 - 0.060: 527 0.060 - 0.091: 174 0.091 - 0.121: 108 0.121 - 0.151: 19 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA HIS D 216 " pdb=" N HIS D 216 " pdb=" C HIS D 216 " pdb=" CB HIS D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE G 263 " pdb=" N ILE G 263 " pdb=" C ILE G 263 " pdb=" CB ILE G 263 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA HIS B 216 " pdb=" N HIS B 216 " pdb=" C HIS B 216 " pdb=" CB HIS B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 2079 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 101 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" CD GLU E 101 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU E 101 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU E 101 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 277 " -0.011 2.00e-02 2.50e+03 1.73e-02 5.23e+00 pdb=" CG PHE B 277 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 277 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 277 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 277 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 277 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 277 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 101 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" CD GLU H 101 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU H 101 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU H 101 " -0.012 2.00e-02 2.50e+03 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 179 2.61 - 3.19: 11653 3.19 - 3.76: 22062 3.76 - 4.33: 32380 4.33 - 4.90: 53797 Nonbonded interactions: 120071 Sorted by model distance: nonbonded pdb=" OD2 ASP B 377 " pdb="FE FE B 503 " model vdw 2.043 2.260 nonbonded pdb=" OD2 ASP D 377 " pdb="FE FE D 503 " model vdw 2.043 2.260 nonbonded pdb=" OD2 ASP G 377 " pdb="FE FE G 503 " model vdw 2.043 2.260 nonbonded pdb=" OD1 ASP G 377 " pdb="FE FE G 503 " model vdw 2.055 2.260 nonbonded pdb=" OD1 ASP B 377 " pdb="FE FE B 503 " model vdw 2.058 2.260 ... (remaining 120066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 3 through 229 or resid 231 through 437 or resid 501 throug \ h 503)) selection = (chain 'D' and (resid 3 through 229 or resid 231 through 437 or resid 501 throug \ h 503)) selection = (chain 'G' and (resid 3 through 229 or resid 231 through 437 or resid 501 throug \ h 503)) } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.170 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 49.330 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.003 0.044 14754 Z= 0.208 Angle : 0.588 12.109 19992 Z= 0.320 Chirality : 0.043 0.151 2082 Planarity : 0.005 0.043 2634 Dihedral : 16.316 84.781 5412 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 21.54 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1773 helix: 0.78 (0.23), residues: 549 sheet: 0.66 (0.29), residues: 309 loop : -0.05 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 429 HIS 0.004 0.001 HIS B 216 PHE 0.039 0.001 PHE B 277 TYR 0.013 0.001 TYR G 426 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.634 Fit side-chains outliers start: 23 outliers final: 21 residues processed: 188 average time/residue: 1.4796 time to fit residues: 302.0066 Evaluate side-chains 183 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 1 average time/residue: 0.1722 time to fit residues: 2.5189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14754 Z= 0.129 Angle : 0.475 7.600 19992 Z= 0.252 Chirality : 0.041 0.141 2082 Planarity : 0.004 0.040 2634 Dihedral : 4.299 31.622 1992 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.66 % Favored : 97.22 % Rotamer: Outliers : 2.77 % Allowed : 20.69 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1773 helix: 1.02 (0.23), residues: 555 sheet: 0.70 (0.29), residues: 309 loop : 0.13 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 429 HIS 0.003 0.001 HIS G 216 PHE 0.028 0.001 PHE B 277 TYR 0.007 0.001 TYR D 128 ARG 0.003 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.664 Fit side-chains outliers start: 42 outliers final: 17 residues processed: 208 average time/residue: 1.4338 time to fit residues: 324.3038 Evaluate side-chains 181 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.7045 time to fit residues: 3.8911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.0020 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14754 Z= 0.131 Angle : 0.470 7.107 19992 Z= 0.248 Chirality : 0.041 0.142 2082 Planarity : 0.004 0.045 2634 Dihedral : 4.146 28.780 1992 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.78 % Favored : 97.05 % Rotamer: Outliers : 2.57 % Allowed : 21.08 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1773 helix: 1.16 (0.23), residues: 555 sheet: 0.73 (0.29), residues: 309 loop : 0.20 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 PHE 0.037 0.001 PHE B 277 TYR 0.010 0.001 TYR B 426 ARG 0.003 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.760 Fit side-chains outliers start: 39 outliers final: 20 residues processed: 204 average time/residue: 1.4551 time to fit residues: 323.0657 Evaluate side-chains 187 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.5633 time to fit residues: 4.3205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 chunk 140 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14754 Z= 0.304 Angle : 0.562 10.343 19992 Z= 0.297 Chirality : 0.044 0.163 2082 Planarity : 0.005 0.048 2634 Dihedral : 4.647 29.528 1992 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.40 % Favored : 96.43 % Rotamer: Outliers : 3.62 % Allowed : 20.16 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1773 helix: 0.82 (0.23), residues: 555 sheet: 0.70 (0.28), residues: 309 loop : 0.08 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 429 HIS 0.005 0.001 HIS B 311 PHE 0.033 0.002 PHE B 277 TYR 0.015 0.001 TYR B 426 ARG 0.005 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 168 time to evaluate : 2.091 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 21 residues processed: 208 average time/residue: 1.5582 time to fit residues: 350.9695 Evaluate side-chains 189 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 3 average time/residue: 0.2591 time to fit residues: 3.4332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN A 97 GLN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14754 Z= 0.393 Angle : 0.611 11.423 19992 Z= 0.325 Chirality : 0.047 0.189 2082 Planarity : 0.005 0.048 2634 Dihedral : 4.920 32.094 1992 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.40 % Favored : 96.43 % Rotamer: Outliers : 3.36 % Allowed : 20.29 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1773 helix: 0.66 (0.23), residues: 549 sheet: 0.12 (0.26), residues: 369 loop : -0.04 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 429 HIS 0.006 0.001 HIS G 311 PHE 0.032 0.002 PHE B 277 TYR 0.016 0.002 TYR B 426 ARG 0.005 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 164 time to evaluate : 1.882 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 26 residues processed: 196 average time/residue: 1.5596 time to fit residues: 331.5638 Evaluate side-chains 189 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 0.2302 time to fit residues: 4.0173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.0010 chunk 41 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14754 Z= 0.285 Angle : 0.568 12.599 19992 Z= 0.301 Chirality : 0.044 0.165 2082 Planarity : 0.005 0.047 2634 Dihedral : 4.783 32.325 1992 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 2.64 % Allowed : 21.01 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1773 helix: 0.69 (0.23), residues: 549 sheet: 0.62 (0.28), residues: 309 loop : -0.10 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 429 HIS 0.004 0.001 HIS A 112 PHE 0.035 0.002 PHE B 277 TYR 0.014 0.001 TYR B 426 ARG 0.005 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.857 Fit side-chains outliers start: 40 outliers final: 24 residues processed: 194 average time/residue: 1.5054 time to fit residues: 317.1639 Evaluate side-chains 188 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 4 average time/residue: 0.4427 time to fit residues: 4.2985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14754 Z= 0.260 Angle : 0.556 10.751 19992 Z= 0.295 Chirality : 0.044 0.159 2082 Planarity : 0.005 0.046 2634 Dihedral : 4.725 32.186 1992 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.23 % Favored : 96.60 % Rotamer: Outliers : 2.17 % Allowed : 21.48 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1773 helix: 0.69 (0.23), residues: 552 sheet: 0.63 (0.29), residues: 309 loop : -0.05 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 429 HIS 0.004 0.001 HIS A 112 PHE 0.032 0.002 PHE B 277 TYR 0.020 0.001 TYR B 426 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 1.835 Fit side-chains outliers start: 33 outliers final: 25 residues processed: 191 average time/residue: 1.5559 time to fit residues: 322.7754 Evaluate side-chains 189 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 4 average time/residue: 0.2545 time to fit residues: 3.8254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 8.9990 chunk 50 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14754 Z= 0.233 Angle : 0.545 9.703 19992 Z= 0.289 Chirality : 0.043 0.156 2082 Planarity : 0.004 0.045 2634 Dihedral : 4.656 31.454 1992 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 2.04 % Allowed : 22.20 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1773 helix: 0.72 (0.23), residues: 552 sheet: 0.64 (0.29), residues: 309 loop : -0.01 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 429 HIS 0.004 0.001 HIS A 112 PHE 0.031 0.001 PHE B 277 TYR 0.019 0.001 TYR B 426 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 1.719 Fit side-chains outliers start: 31 outliers final: 23 residues processed: 195 average time/residue: 1.5214 time to fit residues: 322.6818 Evaluate side-chains 189 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 3 average time/residue: 0.2387 time to fit residues: 3.2801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 102 optimal weight: 0.0020 chunk 165 optimal weight: 10.0000 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN A 97 GLN E 97 GLN G 37 HIS H 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14754 Z= 0.138 Angle : 0.513 12.867 19992 Z= 0.267 Chirality : 0.041 0.168 2082 Planarity : 0.004 0.043 2634 Dihedral : 4.273 28.556 1992 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.61 % Favored : 97.22 % Rotamer: Outliers : 1.58 % Allowed : 22.86 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1773 helix: 0.95 (0.23), residues: 555 sheet: 0.54 (0.27), residues: 339 loop : 0.13 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 429 HIS 0.003 0.001 HIS B 216 PHE 0.029 0.001 PHE B 277 TYR 0.011 0.001 TYR B 426 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.679 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 197 average time/residue: 1.4476 time to fit residues: 310.8992 Evaluate side-chains 186 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.1322 time to fit residues: 2.4921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14754 Z= 0.211 Angle : 0.546 11.407 19992 Z= 0.286 Chirality : 0.043 0.185 2082 Planarity : 0.004 0.044 2634 Dihedral : 4.437 28.530 1992 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 1.38 % Allowed : 22.86 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1773 helix: 0.82 (0.23), residues: 552 sheet: 0.56 (0.27), residues: 339 loop : 0.12 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 429 HIS 0.004 0.001 HIS A 112 PHE 0.029 0.001 PHE B 277 TYR 0.016 0.001 TYR B 426 ARG 0.005 0.000 ARG D 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.660 Fit side-chains outliers start: 21 outliers final: 18 residues processed: 183 average time/residue: 1.5158 time to fit residues: 300.6323 Evaluate side-chains 183 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 1 average time/residue: 0.1868 time to fit residues: 2.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN A 97 GLN E 97 GLN H 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.082327 restraints weight = 43805.756| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.29 r_work: 0.2855 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14754 Z= 0.292 Angle : 0.584 11.577 19992 Z= 0.308 Chirality : 0.045 0.197 2082 Planarity : 0.005 0.047 2634 Dihedral : 4.706 29.565 1992 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 1.52 % Allowed : 22.79 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1773 helix: 0.66 (0.23), residues: 552 sheet: 0.53 (0.27), residues: 339 loop : 0.05 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 429 HIS 0.005 0.001 HIS G 311 PHE 0.029 0.002 PHE B 277 TYR 0.021 0.001 TYR B 426 ARG 0.005 0.000 ARG D 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5345.75 seconds wall clock time: 95 minutes 48.32 seconds (5748.32 seconds total)