Starting phenix.real_space_refine on Thu Nov 16 14:36:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/11_2023/7pbd_13290_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/11_2023/7pbd_13290.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/11_2023/7pbd_13290_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/11_2023/7pbd_13290_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/11_2023/7pbd_13290_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/11_2023/7pbd_13290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/11_2023/7pbd_13290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/11_2023/7pbd_13290_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/11_2023/7pbd_13290_updated.pdb" } resolution = 3.04 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= 0.022 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9617 2.51 5 N 2423 2.21 5 O 2698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 14822 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" 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: "B" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2749 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} 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: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 320} 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: "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: "G" 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 chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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 chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 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 chiralities: 1 Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.83, per 1000 atoms: 0.53 Number of scatterers: 14822 At special positions: 0 Unit cell: (94.5, 120.75, 135.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2698 8.00 N 2423 7.00 C 9617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " distance=2.03 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 Atom "HETATM14820 O5 NAG D 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14777 O5 NAG A 802 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 802 " - " ASN A 111 " " NAG D 502 " - " ASN D 111 " " NAG E 501 " - " ASN E 80 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN C 80 " " NAG K 1 " - " ASN E 149 " Time building additional restraints: 6.48 Conformation dependent library (CDL) restraints added in 2.6 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 17 sheets defined 36.4% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 14 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 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 592 through 614 removed outlier: 4.667A pdb=" N LEU A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Proline residue: A 601 - end of helix removed outlier: 3.922A pdb=" N PHE A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 644 removed outlier: 4.110A pdb=" N SER A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 681 removed outlier: 4.772A pdb=" N LYS A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER A 681 " --> pdb=" O TYR A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 714 Proline residue: A 698 - end of helix Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 219 through 241 removed outlier: 5.133A pdb=" N MET B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix removed outlier: 4.024A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 4.548A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 307 Processing helix chain 'B' and resid 415 through 446 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 10 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 174 Processing helix chain 'C' and resid 221 through 224 No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.942A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 280 through 307 removed outlier: 3.703A pdb=" N ALA C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 446 removed outlier: 3.798A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.550A pdb=" N LEU E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) 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 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 242 removed outlier: 4.870A pdb=" N MET E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 247 through 269 Processing helix chain 'E' and resid 282 through 307 Processing helix chain 'E' and resid 416 through 446 Proline residue: E 432 - end of helix Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 89 through 92 No H-bonds generated for 'chain 'D' and resid 89 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 246 removed outlier: 4.157A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 252 through 275 Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 345 Proline residue: D 330 - end of helix Processing helix chain 'F' and resid 415 through 417 No H-bonds generated for 'chain 'F' and resid 415 through 417' 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 sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.983A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLU A 170 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 41 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 46 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 101 Processing sheet with id= C, first strand: chain 'A' and resid 196 through 204 Processing sheet with id= D, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.421A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.824A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.740A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.105A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.994A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.385A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.802A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.752A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.010A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= N, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= O, first strand: chain 'D' and resid 196 through 204 Processing sheet with id= P, first strand: chain 'F' and resid 406 through 410 Processing sheet with id= Q, first strand: chain 'F' and resid 506 through 508 removed outlier: 6.514A pdb=" N ARG F 425 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE F 434 " --> pdb=" O ARG F 425 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1998 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: 4.58 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4532 1.34 - 1.46: 4052 1.46 - 1.58: 6469 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 15199 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" N ILE C 423 " pdb=" CA ILE C 423 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.25e-02 6.40e+03 5.00e+00 bond pdb=" N TRP C 426 " pdb=" CA TRP C 426 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.21e-02 6.83e+03 4.79e+00 bond pdb=" CA ALA C 420 " pdb=" CB ALA C 420 " ideal model delta sigma weight residual 1.536 1.501 0.034 1.65e-02 3.67e+03 4.32e+00 bond pdb=" CA ALA C 422 " pdb=" CB ALA C 422 " ideal model delta sigma weight residual 1.530 1.498 0.032 1.57e-02 4.06e+03 4.22e+00 ... (remaining 15194 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.51: 399 106.51 - 113.45: 8291 113.45 - 120.39: 5869 120.39 - 127.32: 5925 127.32 - 134.26: 173 Bond angle restraints: 20657 Sorted by residual: angle pdb=" N ILE E 281 " pdb=" CA ILE E 281 " pdb=" C ILE E 281 " ideal model delta sigma weight residual 112.96 107.15 5.81 1.00e+00 1.00e+00 3.38e+01 angle pdb=" N ALA C 420 " pdb=" CA ALA C 420 " pdb=" C ALA C 420 " ideal model delta sigma weight residual 112.93 107.44 5.49 1.33e+00 5.65e-01 1.70e+01 angle pdb=" C LYS F 452 " pdb=" N ASP F 453 " pdb=" CA ASP F 453 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" N ALA C 421 " pdb=" CA ALA C 421 " pdb=" C ALA C 421 " ideal model delta sigma weight residual 111.75 106.95 4.80 1.28e+00 6.10e-01 1.41e+01 angle pdb=" CA ASP F 453 " pdb=" CB ASP F 453 " pdb=" CG ASP F 453 " ideal model delta sigma weight residual 112.60 116.09 -3.49 1.00e+00 1.00e+00 1.22e+01 ... (remaining 20652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7989 18.00 - 35.99: 659 35.99 - 53.99: 86 53.99 - 71.99: 17 71.99 - 89.98: 8 Dihedral angle restraints: 8759 sinusoidal: 3493 harmonic: 5266 Sorted by residual: dihedral pdb=" CB CYS D 139 " pdb=" SG CYS D 139 " pdb=" SG CYS D 153 " pdb=" CB CYS D 153 " ideal model delta sinusoidal sigma weight residual 93.00 42.28 50.72 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CA CYS E 150 " pdb=" C CYS E 150 " pdb=" N THR E 151 " pdb=" CA THR E 151 " ideal model delta harmonic sigma weight residual 180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N GLU B 153 " pdb=" CA GLU B 153 " ideal model delta harmonic sigma weight residual -180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 8756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.450: 2374 0.450 - 0.901: 8 0.901 - 1.351: 1 1.351 - 1.802: 2 1.802 - 2.252: 2 Chirality restraints: 2387 Sorted by residual: 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 -0.15 -2.25 2.00e-02 2.50e+03 1.27e+04 chirality pdb=" C1 MAN H 5 " pdb=" O6 BMA H 3 " pdb=" C2 MAN H 5 " pdb=" O5 MAN H 5 " both_signs ideal model delta sigma weight residual False 2.40 0.45 1.95 2.00e-02 2.50e+03 9.47e+03 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.64 -1.76 2.00e-02 2.50e+03 7.76e+03 ... (remaining 2384 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 80 " -0.132 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" CG ASN C 80 " 0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN C 80 " -0.135 2.00e-02 2.50e+03 pdb=" ND2 ASN C 80 " 0.513 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 80 " 0.238 2.00e-02 2.50e+03 2.46e-01 7.58e+02 pdb=" CG ASN E 80 " -0.116 2.00e-02 2.50e+03 pdb=" OD1 ASN E 80 " -0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN E 80 " -0.365 2.00e-02 2.50e+03 pdb=" C1 NAG E 501 " 0.309 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 149 " 0.137 2.00e-02 2.50e+03 1.44e-01 2.58e+02 pdb=" CG ASN C 149 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN C 149 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN C 149 " -0.218 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.179 2.00e-02 2.50e+03 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 173 2.63 - 3.20: 13478 3.20 - 3.76: 22665 3.76 - 4.33: 31842 4.33 - 4.90: 53308 Nonbonded interactions: 121466 Sorted by model distance: nonbonded pdb=" OE2 GLU B 179 " pdb=" OG SER F 446 " model vdw 2.062 2.440 nonbonded pdb=" OH TYR B 97 " pdb=" OE2 GLU B 155 " model vdw 2.090 2.440 nonbonded pdb=" O TYR B 304 " pdb=" OG SER B 308 " model vdw 2.179 2.440 nonbonded pdb=" ND2 ASN D 88 " pdb=" O PRO D 115 " model vdw 2.203 2.520 nonbonded pdb=" OE2 GLU B 153 " pdb=" NE ARG B 207 " model vdw 2.206 2.520 ... (remaining 121461 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 'D' } ncs_group { reference = (chain 'B' and (resid 8 through 308 or resid 419 through 447)) selection = chain 'C' selection = (chain 'E' and (resid 8 through 308 or resid 419 through 447)) } ncs_group { reference = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' } 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 7.430 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 40.860 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.005 0.052 15199 Z= 0.298 Angle : 0.756 9.846 20657 Z= 0.379 Chirality : 0.101 2.252 2387 Planarity : 0.004 0.052 2536 Dihedral : 13.105 89.981 5357 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1764 helix: 1.63 (0.22), residues: 595 sheet: -0.66 (0.24), residues: 461 loop : -0.61 (0.24), residues: 708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.765 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2236 time to fit residues: 60.8620 Evaluate side-chains 132 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.644 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 0.1980 chunk 159 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15199 Z= 0.292 Angle : 0.618 11.533 20657 Z= 0.306 Chirality : 0.045 0.397 2387 Planarity : 0.004 0.040 2536 Dihedral : 4.677 40.582 2008 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 0.82 % Allowed : 6.44 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1764 helix: 1.88 (0.21), residues: 599 sheet: -0.45 (0.24), residues: 464 loop : -0.56 (0.24), residues: 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.865 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 146 average time/residue: 0.2396 time to fit residues: 55.6008 Evaluate side-chains 132 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1499 time to fit residues: 3.9559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 108 optimal weight: 0.0670 chunk 44 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15199 Z= 0.234 Angle : 0.563 11.285 20657 Z= 0.280 Chirality : 0.042 0.352 2387 Planarity : 0.003 0.034 2536 Dihedral : 4.515 37.635 2008 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.57 % Allowed : 8.91 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1764 helix: 2.06 (0.21), residues: 600 sheet: -0.33 (0.24), residues: 458 loop : -0.53 (0.24), residues: 706 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.808 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 145 average time/residue: 0.2333 time to fit residues: 53.9988 Evaluate side-chains 130 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1491 time to fit residues: 3.7617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 HIS D 308 ASN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15199 Z= 0.451 Angle : 0.658 13.890 20657 Z= 0.329 Chirality : 0.045 0.370 2387 Planarity : 0.004 0.038 2536 Dihedral : 4.792 38.150 2008 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.52 % Allowed : 10.17 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1764 helix: 1.94 (0.21), residues: 601 sheet: -0.53 (0.23), residues: 468 loop : -0.57 (0.24), residues: 695 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 2.001 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 137 average time/residue: 0.2622 time to fit residues: 56.6070 Evaluate side-chains 133 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1474 time to fit residues: 5.9021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 9.9990 chunk 2 optimal weight: 0.0170 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15199 Z= 0.229 Angle : 0.559 7.602 20657 Z= 0.280 Chirality : 0.042 0.364 2387 Planarity : 0.003 0.041 2536 Dihedral : 4.581 35.160 2008 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.57 % Allowed : 11.88 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1764 helix: 2.08 (0.21), residues: 601 sheet: -0.31 (0.24), residues: 454 loop : -0.55 (0.24), residues: 709 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 1.687 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 140 average time/residue: 0.2429 time to fit residues: 54.3815 Evaluate side-chains 128 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1494 time to fit residues: 3.1160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 170 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15199 Z= 0.173 Angle : 0.543 7.988 20657 Z= 0.271 Chirality : 0.042 0.359 2387 Planarity : 0.003 0.042 2536 Dihedral : 4.421 31.178 2008 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.07 % Allowed : 12.38 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1764 helix: 2.30 (0.22), residues: 592 sheet: -0.17 (0.24), residues: 448 loop : -0.46 (0.24), residues: 724 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.842 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 142 average time/residue: 0.2419 time to fit residues: 55.6093 Evaluate side-chains 135 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1717 time to fit residues: 4.0279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15199 Z= 0.260 Angle : 0.563 9.093 20657 Z= 0.281 Chirality : 0.042 0.364 2387 Planarity : 0.003 0.042 2536 Dihedral : 4.444 30.427 2008 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.01 % Allowed : 12.70 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1764 helix: 2.25 (0.21), residues: 593 sheet: -0.12 (0.24), residues: 453 loop : -0.44 (0.24), residues: 718 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.655 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 137 average time/residue: 0.2410 time to fit residues: 52.6448 Evaluate side-chains 137 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1549 time to fit residues: 5.0096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15199 Z= 0.182 Angle : 0.570 17.911 20657 Z= 0.281 Chirality : 0.042 0.358 2387 Planarity : 0.003 0.043 2536 Dihedral : 4.354 27.437 2008 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.51 % Allowed : 13.39 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1764 helix: 2.32 (0.22), residues: 591 sheet: -0.04 (0.24), residues: 449 loop : -0.41 (0.24), residues: 724 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.697 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 135 average time/residue: 0.2411 time to fit residues: 51.9567 Evaluate side-chains 136 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1536 time to fit residues: 3.9644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 103 optimal weight: 0.0970 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15199 Z= 0.191 Angle : 0.545 8.991 20657 Z= 0.272 Chirality : 0.042 0.360 2387 Planarity : 0.003 0.044 2536 Dihedral : 4.298 25.092 2008 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 0.44 % Allowed : 13.39 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1764 helix: 2.31 (0.22), residues: 592 sheet: -0.02 (0.24), residues: 447 loop : -0.37 (0.24), residues: 725 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 1.712 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 134 average time/residue: 0.2392 time to fit residues: 50.9611 Evaluate side-chains 133 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1800 time to fit residues: 3.0567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 4.9990 chunk 102 optimal weight: 0.0470 chunk 79 optimal weight: 0.0020 chunk 116 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 0.4886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15199 Z= 0.155 Angle : 0.575 16.752 20657 Z= 0.282 Chirality : 0.042 0.355 2387 Planarity : 0.003 0.045 2536 Dihedral : 4.246 21.696 2008 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 0.06 % Allowed : 13.96 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.21), residues: 1764 helix: 2.31 (0.22), residues: 591 sheet: 0.16 (0.25), residues: 440 loop : -0.34 (0.24), residues: 733 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.750 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.2574 time to fit residues: 56.1567 Evaluate side-chains 131 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.067988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053635 restraints weight = 48282.049| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.53 r_work: 0.2852 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15199 Z= 0.242 Angle : 0.602 19.856 20657 Z= 0.294 Chirality : 0.043 0.361 2387 Planarity : 0.003 0.044 2536 Dihedral : 4.300 22.223 2008 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 0.25 % Allowed : 14.09 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1764 helix: 2.29 (0.22), residues: 592 sheet: 0.06 (0.24), residues: 454 loop : -0.34 (0.24), residues: 718 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2776.70 seconds wall clock time: 51 minutes 49.23 seconds (3109.23 seconds total)