Starting phenix.real_space_refine on Fri Feb 16 21:51:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc0_13315/02_2024/7pc0_13315_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc0_13315/02_2024/7pc0_13315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc0_13315/02_2024/7pc0_13315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc0_13315/02_2024/7pc0_13315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc0_13315/02_2024/7pc0_13315_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pc0_13315/02_2024/7pc0_13315_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 893 atoms to isotropic. 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 Zn 1 6.06 5 S 104 5.16 5 C 10181 2.51 5 N 2582 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15748 Number of models: 1 Model: "" Number of chains: 17 Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Chain: "A" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2695 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 319} Chain: "B" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "K" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 518 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 497 Classifications: {'peptide': 67} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 5, 'TRANS': 61} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' ZN': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {'HEX': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.70, per 1000 atoms: 0.55 Number of scatterers: 15748 At special positions: 0 Unit cell: (97.11, 137.78, 125.33, 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) Zn 1 29.99 S 104 16.00 O 2880 8.00 N 2582 7.00 C 10181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS K 3 " - pdb=" SG CYS K 20 " distance=2.03 Simple disulfide: pdb=" SG CYS K 3 " - pdb=" SG CYS K 62 " distance=2.05 Simple disulfide: pdb=" SG CYS K 14 " - pdb=" SG CYS K 41 " distance=2.03 Simple disulfide: pdb=" SG CYS K 20 " - pdb=" SG CYS K 57 " distance=2.06 Simple disulfide: pdb=" SG CYS K 20 " - pdb=" SG CYS K 62 " distance=2.02 Simple disulfide: pdb=" SG CYS K 26 " - pdb=" SG CYS K 30 " distance=2.04 Simple disulfide: pdb=" SG CYS K 45 " - pdb=" SG CYS K 56 " distance=2.04 Simple disulfide: pdb=" SG CYS K 57 " - pdb=" SG CYS K 62 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 20 " distance=2.03 Simple disulfide: pdb=" SG CYS L 14 " - pdb=" SG CYS L 41 " distance=2.04 Simple disulfide: pdb=" SG CYS L 20 " - pdb=" SG CYS L 57 " distance=2.05 Simple disulfide: pdb=" SG CYS L 20 " - pdb=" SG CYS L 62 " distance=2.03 Simple disulfide: pdb=" SG CYS L 26 " - pdb=" SG CYS L 30 " distance=2.03 Simple disulfide: pdb=" SG CYS L 45 " - pdb=" SG CYS L 56 " distance=2.03 Simple disulfide: pdb=" SG CYS L 57 " - pdb=" SG CYS L 62 " distance=2.02 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 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 7 " " MAN G 4 " - " MAN G 5 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " MAN G 4 " - " MAN G 6 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG C 501 " - " ASN C 80 " " NAG E 501 " - " ASN E 80 " " NAG G 1 " - " ASN B 149 " " NAG H 1 " - " ASN B 80 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN E 149 " Time building additional restraints: 6.67 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 267 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS E 267 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS C 267 " 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 19 sheets defined 33.4% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'F' and resid 415 through 418 Processing helix chain 'F' and resid 449 through 451 No H-bonds generated for 'chain 'F' and resid 449 through 451' Processing helix chain 'F' and resid 475 through 477 No H-bonds generated for 'chain 'F' and resid 475 through 477' Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.044A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 175 through 178 No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 224 through 247 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 252 through 276 Processing helix chain 'A' and resid 287 through 310 removed outlier: 3.611A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 414 Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 221 through 241 Proline residue: B 228 - end of helix removed outlier: 3.634A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 Processing helix chain 'B' and resid 280 through 307 Processing helix chain 'B' and resid 420 through 445 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 226 through 241 Processing helix chain 'C' and resid 247 through 271 Processing helix chain 'C' and resid 280 through 307 Processing helix chain 'C' and resid 420 through 445 Proline residue: C 432 - end of helix Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 171 through 174 Processing helix chain 'E' and resid 221 through 241 Proline residue: E 228 - end of helix removed outlier: 4.118A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 Processing helix chain 'E' and resid 280 through 307 Processing helix chain 'E' and resid 420 through 446 Proline residue: E 432 - end of helix Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 231 through 246 removed outlier: 4.191A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 Processing helix chain 'D' and resid 285 through 309 Processing helix chain 'D' and resid 315 through 417 removed outlier: 3.651A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix Processing helix chain 'K' and resid 67 through 69 No H-bonds generated for 'chain 'K' and resid 67 through 69' Processing sheet with id= A, first strand: chain 'F' and resid 5 through 7 Processing sheet with id= B, first strand: chain 'F' and resid 506 through 508 removed outlier: 3.671A pdb=" N VAL F 480 " --> pdb=" O GLN F 426 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.300A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLU A 170 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 41 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 99 through 101 Processing sheet with id= E, first strand: chain 'A' and resid 196 through 204 Processing sheet with id= F, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.127A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 105 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 103 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.803A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.310A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.525A pdb=" N LEU B 125 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.162A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.747A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.176A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.430A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE E 105 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.934A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.348A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 96 through 98 removed outlier: 6.437A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 167 through 171 removed outlier: 5.852A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.281A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 19 through 25 701 hydrogen bonds defined for protein. 2025 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: 6.59 Time building geometry restraints manager: 7.10 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: 4852 1.35 - 1.48: 4506 1.48 - 1.61: 6622 1.61 - 1.73: 0 1.73 - 1.86: 166 Bond restraints: 16146 Sorted by residual: bond pdb=" CG HSM B 601 " pdb=" ND1 HSM B 601 " ideal model delta sigma weight residual 1.383 1.314 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" CD2 HSM B 601 " pdb=" NE2 HSM B 601 " ideal model delta sigma weight residual 1.376 1.314 0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.40e+00 ... (remaining 16141 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.02: 278 105.02 - 112.27: 8159 112.27 - 119.52: 5244 119.52 - 126.78: 8018 126.78 - 134.03: 250 Bond angle restraints: 21949 Sorted by residual: angle pdb=" CA THR L 6 " pdb=" CB THR L 6 " pdb=" CG2 THR L 6 " ideal model delta sigma weight residual 110.50 119.61 -9.11 1.70e+00 3.46e-01 2.87e+01 angle pdb=" OG1 THR L 6 " pdb=" CB THR L 6 " pdb=" CG2 THR L 6 " ideal model delta sigma weight residual 109.30 119.63 -10.33 2.00e+00 2.50e-01 2.67e+01 angle pdb=" N THR K 6 " pdb=" CA THR K 6 " pdb=" C THR K 6 " ideal model delta sigma weight residual 109.81 119.93 -10.12 2.21e+00 2.05e-01 2.10e+01 angle pdb=" CA THR L 6 " pdb=" CB THR L 6 " pdb=" OG1 THR L 6 " ideal model delta sigma weight residual 109.60 115.25 -5.65 1.50e+00 4.44e-01 1.42e+01 angle pdb=" CA CYS K 62 " pdb=" CB CYS K 62 " pdb=" SG CYS K 62 " ideal model delta sigma weight residual 114.40 121.91 -7.51 2.30e+00 1.89e-01 1.07e+01 ... (remaining 21944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.75: 9346 25.75 - 51.50: 398 51.50 - 77.24: 44 77.24 - 102.99: 26 102.99 - 128.74: 17 Dihedral angle restraints: 9831 sinusoidal: 4210 harmonic: 5621 Sorted by residual: dihedral pdb=" CB CYS K 20 " pdb=" SG CYS K 20 " pdb=" SG CYS K 62 " pdb=" CB CYS K 62 " ideal model delta sinusoidal sigma weight residual 93.00 -178.78 -88.22 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS L 20 " pdb=" SG CYS L 20 " pdb=" SG CYS L 57 " pdb=" CB CYS L 57 " ideal model delta sinusoidal sigma weight residual -86.00 -1.98 -84.02 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS L 14 " pdb=" SG CYS L 14 " pdb=" SG CYS L 41 " pdb=" CB CYS L 41 " ideal model delta sinusoidal sigma weight residual 93.00 171.60 -78.60 1 1.00e+01 1.00e-02 7.70e+01 ... (remaining 9828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.042: 2523 1.042 - 2.085: 7 2.085 - 3.127: 2 3.127 - 4.169: 3 4.169 - 5.212: 2 Chirality restraints: 2537 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 -2.81 5.21 2.00e-02 2.50e+03 6.79e+04 chirality pdb=" C1 MAN I 5 " pdb=" O3 MAN I 4 " pdb=" C2 MAN I 5 " pdb=" O5 MAN I 5 " both_signs ideal model delta sigma weight residual False 2.40 -2.61 5.01 2.00e-02 2.50e+03 6.28e+04 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 1.45 -3.85 2.00e-02 2.50e+03 3.70e+04 ... (remaining 2534 not shown) Planarity restraints: 2710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 149 " -0.225 2.00e-02 2.50e+03 2.63e-01 8.63e+02 pdb=" CG ASN B 149 " 0.104 2.00e-02 2.50e+03 pdb=" OD1 ASN B 149 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN B 149 " 0.423 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 149 " -0.145 2.00e-02 2.50e+03 1.46e-01 2.66e+02 pdb=" CG ASN C 149 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN C 149 " 0.069 2.00e-02 2.50e+03 pdb=" ND2 ASN C 149 " 0.205 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 80 " 0.078 2.00e-02 2.50e+03 7.96e-02 7.91e+01 pdb=" CG ASN B 80 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 80 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 80 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.096 2.00e-02 2.50e+03 ... (remaining 2707 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 134 2.58 - 3.16: 13222 3.16 - 3.74: 24243 3.74 - 4.32: 34198 4.32 - 4.90: 58221 Nonbonded interactions: 130018 Sorted by model distance: nonbonded pdb=" O PHE B 221 " pdb=" OG1 THR B 225 " model vdw 2.001 2.440 nonbonded pdb=" O PHE E 221 " pdb=" OG1 THR E 225 " model vdw 2.023 2.440 nonbonded pdb=" OD2 ASP L 8 " pdb=" O3 MAN J 4 " model vdw 2.086 2.440 nonbonded pdb=" OG SER F 7 " pdb=" OG SER F 408 " model vdw 2.091 2.440 nonbonded pdb=" OG SER B 51 " pdb=" OD1 ASP B 56 " model vdw 2.091 2.440 ... (remaining 130013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 416) selection = (chain 'D' and resid 12 through 416) } ncs_group { reference = (chain 'B' and resid 8 through 447) selection = (chain 'C' and resid 8 through 447) selection = (chain 'E' and resid 8 through 447) } ncs_group { reference = (chain 'G' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) } ncs_group { reference = (chain 'K' and resid 1 through 67) selection = chain 'L' } 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=1.00 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 13.840 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 49.390 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.110 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 0.069 16146 Z= 0.276 Angle : 0.744 10.328 21949 Z= 0.372 Chirality : 0.228 5.212 2537 Planarity : 0.004 0.075 2704 Dihedral : 15.410 128.741 6154 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.52 (0.20), residues: 1887 helix: 2.06 (0.21), residues: 593 sheet: -1.78 (0.22), residues: 500 loop : -1.16 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 237 HIS 0.004 0.001 HIS E 267 PHE 0.023 0.002 PHE A 258 TYR 0.027 0.002 TYR B 299 ARG 0.010 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 461 ASN cc_start: 0.7552 (m-40) cc_final: 0.7230 (m-40) REVERT: F 467 TYR cc_start: 0.6638 (m-80) cc_final: 0.6006 (m-80) REVERT: F 468 LEU cc_start: 0.7590 (tp) cc_final: 0.7111 (tp) REVERT: A 63 ASP cc_start: 0.7696 (m-30) cc_final: 0.7441 (m-30) REVERT: A 192 ASP cc_start: 0.7859 (t70) cc_final: 0.7615 (t0) REVERT: A 229 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8377 (mm-40) REVERT: A 274 ARG cc_start: 0.7725 (ttt-90) cc_final: 0.6842 (ttt180) REVERT: B 13 LYS cc_start: 0.9358 (tttm) cc_final: 0.9115 (tptm) REVERT: E 112 LYS cc_start: 0.8772 (tmmt) cc_final: 0.8538 (ttpt) REVERT: E 215 LYS cc_start: 0.8488 (tmtt) cc_final: 0.8056 (tmtt) REVERT: E 224 GLN cc_start: 0.7852 (mp10) cc_final: 0.7570 (mt0) REVERT: E 227 MET cc_start: 0.7838 (mmt) cc_final: 0.7623 (mmt) REVERT: K 18 HIS cc_start: 0.6907 (m90) cc_final: 0.6622 (m-70) REVERT: L 5 ILE cc_start: 0.7383 (mm) cc_final: 0.7085 (mt) REVERT: L 32 ILE cc_start: 0.8053 (tt) cc_final: 0.7761 (pt) outliers start: 0 outliers final: 2 residues processed: 215 average time/residue: 1.3319 time to fit residues: 315.5280 Evaluate side-chains 148 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain B residue 172 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 79 optimal weight: 0.3980 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 0.0670 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN A 189 ASN A 275 ASN C 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16146 Z= 0.247 Angle : 0.670 9.348 21949 Z= 0.325 Chirality : 0.045 0.263 2537 Planarity : 0.004 0.040 2704 Dihedral : 11.548 115.564 2603 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.77 % Allowed : 8.27 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -0.28 (0.20), residues: 1887 helix: 2.15 (0.21), residues: 599 sheet: -1.46 (0.22), residues: 497 loop : -1.11 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 25 HIS 0.003 0.001 HIS E 267 PHE 0.018 0.001 PHE E 221 TYR 0.021 0.001 TYR E 299 ARG 0.004 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.778 Fit side-chains revert: symmetry clash REVERT: F 440 TRP cc_start: 0.7393 (m100) cc_final: 0.6983 (m100) REVERT: F 461 ASN cc_start: 0.7627 (m-40) cc_final: 0.7273 (m-40) REVERT: F 467 TYR cc_start: 0.6520 (m-80) cc_final: 0.6272 (m-80) REVERT: A 192 ASP cc_start: 0.7876 (t70) cc_final: 0.7630 (t0) REVERT: A 213 MET cc_start: 0.8425 (mmm) cc_final: 0.7479 (mmm) REVERT: A 229 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8306 (mm-40) REVERT: C 61 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8680 (ptt) REVERT: E 148 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7576 (mm-40) REVERT: E 155 GLU cc_start: 0.7817 (tt0) cc_final: 0.7595 (tt0) REVERT: E 215 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8089 (tmtt) REVERT: E 274 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8427 (mmtt) REVERT: K 18 HIS cc_start: 0.6902 (m90) cc_final: 0.6586 (m-70) REVERT: K 53 ASP cc_start: 0.8611 (m-30) cc_final: 0.8404 (m-30) REVERT: L 32 ILE cc_start: 0.8020 (tt) cc_final: 0.7819 (pt) outliers start: 30 outliers final: 9 residues processed: 180 average time/residue: 1.2488 time to fit residues: 250.0168 Evaluate side-chains 163 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 171 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN B 113 ASN C 85 ASN E 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16146 Z= 0.185 Angle : 0.607 9.668 21949 Z= 0.296 Chirality : 0.044 0.303 2537 Planarity : 0.003 0.035 2704 Dihedral : 10.273 115.422 2600 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.83 % Allowed : 11.40 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -0.07 (0.20), residues: 1887 helix: 2.31 (0.21), residues: 600 sheet: -1.20 (0.23), residues: 489 loop : -1.09 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 25 HIS 0.003 0.001 HIS E 267 PHE 0.017 0.001 PHE E 221 TYR 0.025 0.001 TYR E 277 ARG 0.003 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: F 461 ASN cc_start: 0.7638 (m-40) cc_final: 0.7254 (m-40) REVERT: F 467 TYR cc_start: 0.6612 (m-80) cc_final: 0.6404 (m-80) REVERT: A 58 MET cc_start: 0.8986 (mtt) cc_final: 0.8761 (mmt) REVERT: A 192 ASP cc_start: 0.7850 (t70) cc_final: 0.7616 (t0) REVERT: A 213 MET cc_start: 0.8463 (mmm) cc_final: 0.7353 (mmm) REVERT: A 229 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8294 (mm-40) REVERT: A 274 ARG cc_start: 0.7609 (ttt-90) cc_final: 0.7386 (ttt90) REVERT: B 49 MET cc_start: 0.7819 (ptt) cc_final: 0.7571 (pp-130) REVERT: B 115 MET cc_start: 0.8601 (ptt) cc_final: 0.8361 (ptm) REVERT: C 49 MET cc_start: 0.7408 (tmm) cc_final: 0.7167 (tmm) REVERT: C 61 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8658 (ptt) REVERT: E 18 LYS cc_start: 0.9436 (ttpp) cc_final: 0.9156 (tmmm) REVERT: E 64 GLN cc_start: 0.8666 (mp10) cc_final: 0.8129 (mp10) REVERT: E 215 LYS cc_start: 0.8484 (tmtt) cc_final: 0.8064 (tmtt) REVERT: E 274 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8547 (mmtt) REVERT: E 429 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8368 (mt) REVERT: K 18 HIS cc_start: 0.6824 (m90) cc_final: 0.6541 (m-70) outliers start: 31 outliers final: 9 residues processed: 177 average time/residue: 1.2303 time to fit residues: 242.2051 Evaluate side-chains 162 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 16146 Z= 0.385 Angle : 0.677 11.283 21949 Z= 0.336 Chirality : 0.046 0.265 2537 Planarity : 0.004 0.042 2704 Dihedral : 9.791 112.632 2598 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.60 % Allowed : 12.76 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -0.11 (0.20), residues: 1887 helix: 2.17 (0.21), residues: 609 sheet: -1.24 (0.23), residues: 480 loop : -1.06 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 25 HIS 0.005 0.001 HIS E 119 PHE 0.022 0.002 PHE D 304 TYR 0.023 0.002 TYR B 299 ARG 0.005 0.000 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 154 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7872 (t70) cc_final: 0.7625 (t0) REVERT: A 229 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8405 (mm-40) REVERT: B 49 MET cc_start: 0.7848 (ptt) cc_final: 0.7541 (pp-130) REVERT: C 49 MET cc_start: 0.7493 (tmm) cc_final: 0.7265 (tmm) REVERT: C 61 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8783 (ptt) REVERT: E 18 LYS cc_start: 0.9448 (ttpp) cc_final: 0.9185 (tmmm) REVERT: E 115 MET cc_start: 0.8888 (ptm) cc_final: 0.8640 (ptp) REVERT: E 215 LYS cc_start: 0.8581 (tmtt) cc_final: 0.8153 (tmtt) REVERT: E 274 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8696 (mmtt) REVERT: D 15 PHE cc_start: 0.8167 (m-80) cc_final: 0.7810 (t80) REVERT: K 18 HIS cc_start: 0.6931 (m90) cc_final: 0.6604 (m-70) REVERT: L 38 ASP cc_start: 0.6834 (t0) cc_final: 0.6629 (t0) outliers start: 44 outliers final: 17 residues processed: 183 average time/residue: 1.1682 time to fit residues: 239.2294 Evaluate side-chains 165 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16146 Z= 0.205 Angle : 0.619 11.800 21949 Z= 0.302 Chirality : 0.044 0.295 2537 Planarity : 0.003 0.036 2704 Dihedral : 9.355 111.729 2598 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.07 % Allowed : 14.12 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 0.03 (0.20), residues: 1887 helix: 2.32 (0.21), residues: 600 sheet: -1.10 (0.23), residues: 477 loop : -1.01 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 25 HIS 0.005 0.001 HIS A 110 PHE 0.015 0.001 PHE E 221 TYR 0.023 0.001 TYR E 299 ARG 0.005 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 421 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8165 (ttm) REVERT: F 474 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8404 (mmtm) REVERT: A 192 ASP cc_start: 0.7865 (t70) cc_final: 0.7622 (t0) REVERT: A 229 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8402 (mm-40) REVERT: A 274 ARG cc_start: 0.7802 (ttt-90) cc_final: 0.7556 (ttt-90) REVERT: B 49 MET cc_start: 0.7869 (ptt) cc_final: 0.7553 (pp-130) REVERT: B 286 MET cc_start: 0.7761 (tpp) cc_final: 0.7558 (tpp) REVERT: C 283 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7303 (mpp) REVERT: E 18 LYS cc_start: 0.9438 (ttpp) cc_final: 0.9188 (tmmm) REVERT: E 115 MET cc_start: 0.8883 (ptm) cc_final: 0.8596 (ptp) REVERT: E 155 GLU cc_start: 0.8068 (tt0) cc_final: 0.7178 (tt0) REVERT: E 215 LYS cc_start: 0.8577 (tmtt) cc_final: 0.8143 (tmtt) REVERT: E 429 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8373 (mt) REVERT: D 15 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7706 (t80) REVERT: D 114 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7589 (ppp) REVERT: K 18 HIS cc_start: 0.6816 (m90) cc_final: 0.6508 (m-70) REVERT: L 38 ASP cc_start: 0.6459 (t0) cc_final: 0.6221 (t0) outliers start: 35 outliers final: 15 residues processed: 178 average time/residue: 1.2227 time to fit residues: 242.9133 Evaluate side-chains 157 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 182 optimal weight: 0.0570 chunk 151 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 overall best weight: 2.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN D 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 16146 Z= 0.355 Angle : 0.672 12.638 21949 Z= 0.328 Chirality : 0.045 0.260 2537 Planarity : 0.004 0.035 2704 Dihedral : 9.261 110.604 2598 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.36 % Allowed : 14.71 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -0.02 (0.20), residues: 1887 helix: 2.13 (0.21), residues: 611 sheet: -1.14 (0.23), residues: 484 loop : -0.94 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 237 HIS 0.004 0.001 HIS A 110 PHE 0.019 0.002 PHE D 304 TYR 0.022 0.002 TYR E 299 ARG 0.004 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 145 time to evaluate : 1.919 Fit side-chains revert: symmetry clash REVERT: F 421 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7866 (ttm) REVERT: F 474 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8499 (mptt) REVERT: A 192 ASP cc_start: 0.7864 (t70) cc_final: 0.7614 (t0) REVERT: A 229 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8453 (mm-40) REVERT: A 274 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7673 (ttt-90) REVERT: B 49 MET cc_start: 0.7869 (ptt) cc_final: 0.7602 (pp-130) REVERT: C 286 MET cc_start: 0.8324 (tpp) cc_final: 0.7698 (tpp) REVERT: E 115 MET cc_start: 0.8902 (ptm) cc_final: 0.8653 (ptp) REVERT: E 155 GLU cc_start: 0.8094 (tt0) cc_final: 0.7851 (tt0) REVERT: E 215 LYS cc_start: 0.8557 (tmtt) cc_final: 0.8078 (tmtt) REVERT: D 15 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.8034 (t80) REVERT: D 114 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7578 (ppp) REVERT: K 18 HIS cc_start: 0.6904 (m90) cc_final: 0.6613 (m-70) REVERT: L 38 ASP cc_start: 0.6339 (t0) cc_final: 0.6087 (t0) outliers start: 40 outliers final: 22 residues processed: 167 average time/residue: 1.1913 time to fit residues: 222.4392 Evaluate side-chains 159 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 472 ASN Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 133 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN C 303 ASN D 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16146 Z= 0.185 Angle : 0.624 11.355 21949 Z= 0.302 Chirality : 0.044 0.285 2537 Planarity : 0.003 0.035 2704 Dihedral : 8.825 109.697 2598 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.13 % Allowed : 15.36 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: 0.14 (0.20), residues: 1887 helix: 2.36 (0.21), residues: 598 sheet: -0.91 (0.24), residues: 467 loop : -0.99 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 440 HIS 0.009 0.001 HIS A 110 PHE 0.012 0.001 PHE A 404 TYR 0.024 0.001 TYR C 220 ARG 0.005 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 421 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7992 (ttm) REVERT: F 474 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8403 (mptt) REVERT: A 192 ASP cc_start: 0.7844 (t70) cc_final: 0.7601 (t0) REVERT: A 213 MET cc_start: 0.8562 (mmm) cc_final: 0.7455 (mmm) REVERT: A 229 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8391 (mm-40) REVERT: B 49 MET cc_start: 0.7855 (ptt) cc_final: 0.7600 (pp-130) REVERT: B 286 MET cc_start: 0.7804 (tpp) cc_final: 0.7577 (tpp) REVERT: C 223 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7513 (tm) REVERT: C 286 MET cc_start: 0.8263 (tpp) cc_final: 0.7642 (tpp) REVERT: E 115 MET cc_start: 0.8859 (ptm) cc_final: 0.8584 (ptp) REVERT: D 15 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7980 (t80) REVERT: D 114 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7510 (ppp) REVERT: K 18 HIS cc_start: 0.6847 (m90) cc_final: 0.6525 (m-70) REVERT: L 38 ASP cc_start: 0.6204 (t0) cc_final: 0.5955 (t0) outliers start: 36 outliers final: 20 residues processed: 160 average time/residue: 1.0877 time to fit residues: 196.2947 Evaluate side-chains 158 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain K residue 3 CYS Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 0.0570 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN D 242 GLN D 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16146 Z= 0.193 Angle : 0.634 11.300 21949 Z= 0.305 Chirality : 0.043 0.268 2537 Planarity : 0.003 0.036 2704 Dihedral : 8.542 107.783 2598 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 2.01 % Allowed : 15.53 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.20 (0.20), residues: 1887 helix: 2.40 (0.21), residues: 598 sheet: -0.84 (0.24), residues: 467 loop : -0.97 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 237 HIS 0.003 0.001 HIS E 267 PHE 0.011 0.001 PHE D 304 TYR 0.023 0.001 TYR E 299 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 421 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7995 (ttm) REVERT: F 474 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8637 (mmtt) REVERT: A 192 ASP cc_start: 0.7832 (t70) cc_final: 0.7586 (t0) REVERT: A 213 MET cc_start: 0.8517 (mmm) cc_final: 0.7395 (mmm) REVERT: A 229 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8336 (mm-40) REVERT: A 274 ARG cc_start: 0.7862 (ttt-90) cc_final: 0.7201 (ttt-90) REVERT: B 49 MET cc_start: 0.7857 (ptt) cc_final: 0.7613 (pp-130) REVERT: C 223 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7592 (tm) REVERT: C 286 MET cc_start: 0.8225 (tpp) cc_final: 0.7659 (tpp) REVERT: E 115 MET cc_start: 0.8850 (ptm) cc_final: 0.8568 (ptp) REVERT: D 15 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7983 (t80) REVERT: D 114 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7469 (ppp) REVERT: K 18 HIS cc_start: 0.6849 (m90) cc_final: 0.6542 (m-70) REVERT: L 38 ASP cc_start: 0.6184 (t0) cc_final: 0.5965 (t0) outliers start: 34 outliers final: 20 residues processed: 159 average time/residue: 1.1404 time to fit residues: 204.0329 Evaluate side-chains 158 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 504 GLN A 116 ASN C 303 ASN D 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 16146 Z= 0.377 Angle : 0.695 11.801 21949 Z= 0.340 Chirality : 0.046 0.252 2537 Planarity : 0.004 0.038 2704 Dihedral : 8.561 106.463 2598 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 2.01 % Allowed : 16.07 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.01 (0.20), residues: 1887 helix: 2.11 (0.21), residues: 611 sheet: -1.11 (0.23), residues: 495 loop : -0.88 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 237 HIS 0.004 0.001 HIS A 110 PHE 0.021 0.002 PHE D 304 TYR 0.023 0.002 TYR E 299 ARG 0.004 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 2.010 Fit side-chains revert: symmetry clash REVERT: F 421 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7943 (ttm) REVERT: F 474 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8671 (mmtt) REVERT: A 192 ASP cc_start: 0.7855 (t70) cc_final: 0.7614 (t0) REVERT: A 213 MET cc_start: 0.8517 (mmm) cc_final: 0.7505 (mmm) REVERT: A 229 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8459 (mm-40) REVERT: B 49 MET cc_start: 0.7840 (ptt) cc_final: 0.7598 (pp-130) REVERT: C 223 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7773 (tm) REVERT: C 286 MET cc_start: 0.8369 (tpp) cc_final: 0.7879 (tpp) REVERT: E 115 MET cc_start: 0.8914 (ptm) cc_final: 0.8695 (ptp) REVERT: E 155 GLU cc_start: 0.8182 (tt0) cc_final: 0.7963 (tt0) REVERT: D 15 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.8055 (t80) REVERT: D 114 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7434 (ppp) REVERT: K 18 HIS cc_start: 0.7034 (m90) cc_final: 0.6659 (m-70) outliers start: 34 outliers final: 21 residues processed: 151 average time/residue: 1.2553 time to fit residues: 211.8771 Evaluate side-chains 150 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 159 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 224 GLN C 303 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16146 Z= 0.184 Angle : 0.658 13.295 21949 Z= 0.317 Chirality : 0.044 0.265 2537 Planarity : 0.003 0.039 2704 Dihedral : 8.108 105.516 2598 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 1.71 % Allowed : 16.54 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.15 (0.20), residues: 1887 helix: 2.23 (0.21), residues: 609 sheet: -0.88 (0.24), residues: 470 loop : -0.93 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 237 HIS 0.003 0.001 HIS E 267 PHE 0.011 0.001 PHE A 404 TYR 0.023 0.001 TYR E 299 ARG 0.005 0.000 ARG K 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 2.591 Fit side-chains REVERT: F 421 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7832 (ttm) REVERT: F 474 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8624 (mmtt) REVERT: A 192 ASP cc_start: 0.7829 (t70) cc_final: 0.7588 (t0) REVERT: A 213 MET cc_start: 0.8489 (mmm) cc_final: 0.7294 (mmm) REVERT: A 229 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8345 (mm-40) REVERT: B 49 MET cc_start: 0.7849 (ptt) cc_final: 0.7618 (pp-130) REVERT: C 223 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7404 (tm) REVERT: C 286 MET cc_start: 0.8235 (tpp) cc_final: 0.7676 (tpp) REVERT: E 115 MET cc_start: 0.8870 (ptm) cc_final: 0.8612 (ptp) REVERT: K 18 HIS cc_start: 0.6823 (m90) cc_final: 0.6485 (m-70) outliers start: 29 outliers final: 17 residues processed: 154 average time/residue: 1.1248 time to fit residues: 195.4246 Evaluate side-chains 155 residues out of total 1698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN C 303 ASN D 196 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.080309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.060707 restraints weight = 41428.138| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.31 r_work: 0.2894 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 16146 Z= 0.299 Angle : 0.690 12.859 21949 Z= 0.333 Chirality : 0.045 0.246 2537 Planarity : 0.004 0.038 2704 Dihedral : 8.039 104.330 2598 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.14 % Favored : 94.81 % Rotamer: Outliers : 1.65 % Allowed : 16.95 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.12 (0.20), residues: 1887 helix: 2.21 (0.21), residues: 606 sheet: -0.99 (0.23), residues: 488 loop : -0.85 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP F 440 HIS 0.003 0.001 HIS E 267 PHE 0.016 0.001 PHE D 304 TYR 0.023 0.001 TYR E 299 ARG 0.005 0.000 ARG K 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4812.75 seconds wall clock time: 87 minutes 13.90 seconds (5233.90 seconds total)