Starting phenix.real_space_refine on Sat Mar 16 20:55:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/03_2024/7pbd_13290_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/03_2024/7pbd_13290.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/03_2024/7pbd_13290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/03_2024/7pbd_13290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/03_2024/7pbd_13290_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/03_2024/7pbd_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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: 6.15 Conformation dependent library (CDL) restraints added in 2.8 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: 2.85 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: 4.43 Time building geometry restraints manager: 6.57 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=" CG HSM B 601 " pdb=" ND1 HSM B 601 " ideal model delta sigma weight residual 1.383 1.312 0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CD2 HSM B 601 " pdb=" NE2 HSM B 601 " ideal model delta sigma weight residual 1.376 1.313 0.063 2.00e-02 2.50e+03 9.94e+00 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 ... (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 - 23.44: 8648 23.44 - 46.89: 447 46.89 - 70.33: 37 70.33 - 93.77: 29 93.77 - 117.22: 43 Dihedral angle restraints: 9204 sinusoidal: 3938 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 9201 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 7.350 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 41.670 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.910 ------------------------------------------------------------------------------- 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 0.071 15199 Z= 0.300 Angle : 0.758 9.846 20657 Z= 0.380 Chirality : 0.101 2.252 2387 Planarity : 0.004 0.052 2536 Dihedral : 16.572 117.217 5802 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 237 HIS 0.006 0.001 HIS D 110 PHE 0.023 0.002 PHE A 626 TYR 0.013 0.001 TYR E 157 ARG 0.009 0.000 ARG D 255 *********************** 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 : 1.572 Fit side-chains revert: symmetry clash REVERT: A 597 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 227 MET cc_start: 0.7754 (ppp) cc_final: 0.7422 (ppp) REVERT: C 49 MET cc_start: 0.8388 (ppp) cc_final: 0.7889 (ppp) REVERT: C 90 GLN cc_start: 0.8881 (mp10) cc_final: 0.8574 (mp10) REVERT: E 49 MET cc_start: 0.8276 (mmm) cc_final: 0.7839 (tmm) REVERT: E 282 ASP cc_start: 0.8718 (m-30) cc_final: 0.8505 (t70) REVERT: E 283 MET cc_start: 0.8339 (ttt) cc_final: 0.8114 (ttm) REVERT: D 228 ILE cc_start: 0.9177 (tt) cc_final: 0.8814 (tt) REVERT: F 3 GLN cc_start: 0.8089 (mp10) cc_final: 0.7597 (mp10) REVERT: F 5 GLN cc_start: 0.8079 (mp-120) cc_final: 0.7829 (mm-40) REVERT: F 6 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6684 (tm-30) REVERT: F 405 LEU cc_start: 0.6888 (tt) cc_final: 0.6553 (tp) REVERT: F 412 SER cc_start: 0.8232 (p) cc_final: 0.7515 (p) REVERT: F 414 HIS cc_start: 0.8172 (m90) cc_final: 0.7690 (m90) REVERT: F 456 THR cc_start: 0.9067 (m) cc_final: 0.8406 (p) REVERT: F 470 MET cc_start: 0.8381 (mpp) cc_final: 0.7838 (mpp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2188 time to fit residues: 59.0258 Evaluate side-chains 135 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 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: 1.3984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15199 Z= 0.243 Angle : 0.615 12.206 20657 Z= 0.299 Chirality : 0.046 0.378 2387 Planarity : 0.003 0.040 2536 Dihedral : 11.761 126.404 2453 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 0.76 % Allowed : 6.38 % Favored : 92.86 % 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: 0.42 (0.20), residues: 1764 helix: 1.87 (0.21), residues: 600 sheet: -0.40 (0.24), residues: 448 loop : -0.57 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 241 HIS 0.003 0.001 HIS E 107 PHE 0.017 0.001 PHE E 186 TYR 0.016 0.001 TYR B 299 ARG 0.002 0.000 ARG A 187 *********************** 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: 12 poor density : 142 time to evaluate : 1.689 Fit side-chains REVERT: A 90 MET cc_start: 0.8207 (mmm) cc_final: 0.7996 (tpt) REVERT: A 597 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7793 (tm-30) REVERT: C 49 MET cc_start: 0.8320 (ppp) cc_final: 0.7917 (ppp) REVERT: C 155 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7475 (mm-30) REVERT: E 55 MET cc_start: 0.8772 (mmm) cc_final: 0.8527 (mmm) REVERT: E 283 MET cc_start: 0.8366 (ttt) cc_final: 0.8100 (ttm) REVERT: F 414 HIS cc_start: 0.8190 (m90) cc_final: 0.7699 (m90) REVERT: F 456 THR cc_start: 0.9018 (m) cc_final: 0.8718 (p) REVERT: F 467 TYR cc_start: 0.8101 (m-80) cc_final: 0.7514 (m-80) outliers start: 12 outliers final: 5 residues processed: 147 average time/residue: 0.2291 time to fit residues: 54.4584 Evaluate side-chains 134 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 172 optimal weight: 0.0370 chunk 142 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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: 0.8103 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15199 Z= 0.157 Angle : 0.545 10.673 20657 Z= 0.267 Chirality : 0.043 0.344 2387 Planarity : 0.003 0.036 2536 Dihedral : 9.324 112.138 2453 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.82 % Allowed : 8.34 % Favored : 90.84 % 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: 0.71 (0.21), residues: 1764 helix: 2.18 (0.22), residues: 593 sheet: -0.20 (0.24), residues: 463 loop : -0.47 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 241 HIS 0.004 0.000 HIS D 110 PHE 0.013 0.001 PHE A 666 TYR 0.015 0.001 TYR B 299 ARG 0.003 0.000 ARG F 406 *********************** 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 158 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.546 Fit side-chains REVERT: A 90 MET cc_start: 0.8070 (mmm) cc_final: 0.7853 (tpt) REVERT: A 597 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 49 MET cc_start: 0.8319 (ppp) cc_final: 0.7893 (ppp) REVERT: C 155 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7391 (mm-30) REVERT: E 185 GLN cc_start: 0.8997 (pm20) cc_final: 0.8616 (pm20) REVERT: E 278 VAL cc_start: 0.8635 (p) cc_final: 0.7998 (m) REVERT: E 426 TRP cc_start: 0.8487 (t60) cc_final: 0.8230 (t-100) REVERT: D 213 MET cc_start: 0.8572 (mtm) cc_final: 0.8367 (mtm) REVERT: D 223 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8563 (tt) REVERT: F 414 HIS cc_start: 0.8170 (m90) cc_final: 0.7719 (m90) REVERT: F 456 THR cc_start: 0.9150 (m) cc_final: 0.8786 (p) outliers start: 13 outliers final: 8 residues processed: 153 average time/residue: 0.2212 time to fit residues: 54.0787 Evaluate side-chains 142 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 160 optimal weight: 0.2980 chunk 170 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN D 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1366 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= 0.199 Angle : 0.531 9.527 20657 Z= 0.265 Chirality : 0.043 0.350 2387 Planarity : 0.003 0.040 2536 Dihedral : 8.663 110.936 2453 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.45 % Allowed : 9.03 % Favored : 89.51 % 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: 0.82 (0.21), residues: 1764 helix: 2.29 (0.22), residues: 591 sheet: -0.12 (0.24), residues: 465 loop : -0.43 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 426 HIS 0.003 0.001 HIS D 110 PHE 0.017 0.001 PHE C 293 TYR 0.015 0.001 TYR B 299 ARG 0.002 0.000 ARG D 31 *********************** 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 158 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.743 Fit side-chains REVERT: A 597 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7801 (tm-30) REVERT: B 55 MET cc_start: 0.8817 (mmp) cc_final: 0.8585 (mmp) REVERT: C 49 MET cc_start: 0.8318 (ppp) cc_final: 0.8016 (ppp) REVERT: E 49 MET cc_start: 0.8329 (ttm) cc_final: 0.7728 (tmm) REVERT: E 185 GLN cc_start: 0.8974 (pm20) cc_final: 0.8534 (pm20) REVERT: E 426 TRP cc_start: 0.8477 (t60) cc_final: 0.8238 (t-100) REVERT: D 213 MET cc_start: 0.8575 (mtm) cc_final: 0.8171 (mtm) REVERT: D 223 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8643 (tt) REVERT: F 414 HIS cc_start: 0.8201 (m90) cc_final: 0.7776 (m90) REVERT: F 456 THR cc_start: 0.9144 (m) cc_final: 0.8823 (p) outliers start: 23 outliers final: 10 residues processed: 150 average time/residue: 0.2210 time to fit residues: 53.2475 Evaluate side-chains 140 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 8.9990 chunk 2 optimal weight: 0.0970 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 0.0770 chunk 117 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN D 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15199 Z= 0.238 Angle : 0.542 9.163 20657 Z= 0.270 Chirality : 0.043 0.369 2387 Planarity : 0.003 0.043 2536 Dihedral : 8.182 108.975 2453 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.52 % Allowed : 9.98 % Favored : 88.50 % 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: 0.82 (0.21), residues: 1764 helix: 2.29 (0.22), residues: 593 sheet: -0.12 (0.24), residues: 442 loop : -0.44 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 426 HIS 0.004 0.001 HIS D 110 PHE 0.021 0.001 PHE C 293 TYR 0.016 0.001 TYR B 299 ARG 0.002 0.000 ARG D 31 *********************** 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 159 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.518 Fit side-chains REVERT: A 597 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7881 (tm-30) REVERT: B 55 MET cc_start: 0.8896 (mmp) cc_final: 0.8692 (mmp) REVERT: C 49 MET cc_start: 0.8327 (ppp) cc_final: 0.8011 (ppp) REVERT: C 155 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7612 (mm-30) REVERT: E 49 MET cc_start: 0.8300 (ttm) cc_final: 0.7689 (tmm) REVERT: E 185 GLN cc_start: 0.9015 (pm20) cc_final: 0.8601 (pm20) REVERT: E 426 TRP cc_start: 0.8497 (t60) cc_final: 0.8249 (t-100) REVERT: D 213 MET cc_start: 0.8539 (mtm) cc_final: 0.7996 (mtm) REVERT: D 223 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8672 (tt) REVERT: F 414 HIS cc_start: 0.8264 (m90) cc_final: 0.7864 (m90) REVERT: F 456 THR cc_start: 0.9210 (m) cc_final: 0.8920 (p) outliers start: 24 outliers final: 16 residues processed: 147 average time/residue: 0.2271 time to fit residues: 53.2859 Evaluate side-chains 145 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 170 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 89 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.1622 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= 0.210 Angle : 0.535 8.749 20657 Z= 0.266 Chirality : 0.043 0.380 2387 Planarity : 0.003 0.043 2536 Dihedral : 7.807 105.768 2453 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.39 % Allowed : 10.61 % Favored : 88.00 % 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: 0.86 (0.21), residues: 1764 helix: 2.32 (0.22), residues: 593 sheet: -0.07 (0.24), residues: 442 loop : -0.43 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 426 HIS 0.004 0.001 HIS D 110 PHE 0.020 0.001 PHE C 293 TYR 0.016 0.001 TYR B 299 ARG 0.002 0.000 ARG D 31 *********************** 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 152 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 597 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 55 MET cc_start: 0.8927 (mmp) cc_final: 0.8693 (mmp) REVERT: C 49 MET cc_start: 0.8348 (ppp) cc_final: 0.8041 (ppp) REVERT: E 49 MET cc_start: 0.8297 (ttm) cc_final: 0.7688 (tmm) REVERT: E 185 GLN cc_start: 0.9018 (pm20) cc_final: 0.8629 (pm20) REVERT: E 190 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: D 148 MET cc_start: 0.8568 (mpp) cc_final: 0.8179 (mpp) REVERT: D 213 MET cc_start: 0.8471 (mtm) cc_final: 0.7859 (mtm) REVERT: D 229 GLN cc_start: 0.8568 (tp40) cc_final: 0.8073 (tp40) REVERT: F 414 HIS cc_start: 0.8193 (m90) cc_final: 0.7808 (m90) REVERT: F 456 THR cc_start: 0.9254 (m) cc_final: 0.8976 (p) outliers start: 22 outliers final: 17 residues processed: 139 average time/residue: 0.2297 time to fit residues: 50.4607 Evaluate side-chains 145 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.8144 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15199 Z= 0.247 Angle : 0.544 9.136 20657 Z= 0.272 Chirality : 0.043 0.377 2387 Planarity : 0.003 0.044 2536 Dihedral : 7.321 102.868 2453 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.90 % Allowed : 11.31 % Favored : 86.80 % 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: 2.33 (0.22), residues: 593 sheet: -0.08 (0.24), residues: 447 loop : -0.40 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 237 HIS 0.003 0.001 HIS D 110 PHE 0.020 0.001 PHE C 293 TYR 0.017 0.001 TYR B 299 ARG 0.002 0.000 ARG D 31 *********************** 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 161 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 597 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 55 MET cc_start: 0.8970 (mmp) cc_final: 0.8716 (mmp) REVERT: C 49 MET cc_start: 0.8359 (ppp) cc_final: 0.8044 (ppp) REVERT: E 49 MET cc_start: 0.8297 (ttm) cc_final: 0.7702 (tmm) REVERT: E 185 GLN cc_start: 0.9025 (pm20) cc_final: 0.8683 (pm20) REVERT: E 190 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: D 213 MET cc_start: 0.8502 (mtm) cc_final: 0.8115 (mtm) REVERT: D 229 GLN cc_start: 0.8604 (tp40) cc_final: 0.8107 (tp40) REVERT: F 414 HIS cc_start: 0.8242 (m90) cc_final: 0.7877 (m90) REVERT: F 452 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8309 (tppt) REVERT: F 456 THR cc_start: 0.9274 (m) cc_final: 0.9010 (p) outliers start: 30 outliers final: 21 residues processed: 147 average time/residue: 0.2273 time to fit residues: 52.8788 Evaluate side-chains 150 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8136 moved from start: 0.1792 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= 0.211 Angle : 0.536 9.428 20657 Z= 0.269 Chirality : 0.043 0.367 2387 Planarity : 0.003 0.043 2536 Dihedral : 6.953 98.977 2453 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.58 % Allowed : 11.56 % Favored : 86.86 % 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: 2.33 (0.22), residues: 592 sheet: -0.06 (0.24), residues: 440 loop : -0.35 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 237 HIS 0.004 0.001 HIS D 110 PHE 0.019 0.001 PHE C 293 TYR 0.016 0.001 TYR B 299 ARG 0.002 0.000 ARG D 31 *********************** 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 157 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.871 Fit side-chains REVERT: A 597 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 662 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7798 (t80) REVERT: B 55 MET cc_start: 0.8984 (mmp) cc_final: 0.8731 (mmp) REVERT: C 49 MET cc_start: 0.8371 (ppp) cc_final: 0.8036 (ppp) REVERT: C 286 MET cc_start: 0.8559 (mmp) cc_final: 0.8166 (tpp) REVERT: E 49 MET cc_start: 0.8287 (ttm) cc_final: 0.7699 (tmm) REVERT: E 185 GLN cc_start: 0.9020 (pm20) cc_final: 0.8689 (pm20) REVERT: E 190 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: D 213 MET cc_start: 0.8481 (mtm) cc_final: 0.8039 (mtm) REVERT: D 229 GLN cc_start: 0.8602 (tp40) cc_final: 0.8039 (tp40) REVERT: F 414 HIS cc_start: 0.8232 (m90) cc_final: 0.7875 (m90) REVERT: F 456 THR cc_start: 0.9296 (m) cc_final: 0.9033 (p) outliers start: 25 outliers final: 19 residues processed: 143 average time/residue: 0.2323 time to fit residues: 52.5145 Evaluate side-chains 150 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 68 optimal weight: 0.0270 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 142 optimal weight: 0.1980 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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: 0.8118 moved from start: 0.1870 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= 0.168 Angle : 0.537 10.186 20657 Z= 0.268 Chirality : 0.042 0.354 2387 Planarity : 0.003 0.044 2536 Dihedral : 6.539 92.557 2453 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.45 % Allowed : 11.88 % Favored : 86.67 % 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: 0.96 (0.21), residues: 1764 helix: 2.36 (0.22), residues: 591 sheet: -0.04 (0.24), residues: 443 loop : -0.31 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 237 HIS 0.003 0.000 HIS D 110 PHE 0.018 0.001 PHE C 293 TYR 0.015 0.001 TYR B 299 ARG 0.002 0.000 ARG F 454 *********************** 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 157 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.847 Fit side-chains REVERT: A 581 MET cc_start: 0.8189 (mmm) cc_final: 0.7545 (mmm) REVERT: A 597 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 662 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7757 (t80) REVERT: B 55 MET cc_start: 0.8985 (mmp) cc_final: 0.8744 (mmp) REVERT: C 49 MET cc_start: 0.8412 (ppp) cc_final: 0.8074 (ppp) REVERT: C 286 MET cc_start: 0.8515 (mmp) cc_final: 0.8091 (tpp) REVERT: E 49 MET cc_start: 0.8272 (ttm) cc_final: 0.7701 (tmm) REVERT: E 185 GLN cc_start: 0.9015 (pm20) cc_final: 0.8713 (pm20) REVERT: E 190 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: D 213 MET cc_start: 0.8473 (mtm) cc_final: 0.8024 (mtm) REVERT: F 414 HIS cc_start: 0.8193 (m90) cc_final: 0.7863 (m90) REVERT: F 456 THR cc_start: 0.9319 (m) cc_final: 0.9065 (p) outliers start: 23 outliers final: 18 residues processed: 146 average time/residue: 0.2181 time to fit residues: 51.0409 Evaluate side-chains 151 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15199 Z= 0.155 Angle : 0.530 9.072 20657 Z= 0.264 Chirality : 0.041 0.354 2387 Planarity : 0.003 0.044 2536 Dihedral : 6.025 81.331 2453 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 1.07 % Allowed : 12.51 % Favored : 86.42 % 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: 2.38 (0.22), residues: 591 sheet: -0.04 (0.24), residues: 448 loop : -0.26 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 237 HIS 0.004 0.000 HIS D 110 PHE 0.017 0.001 PHE C 293 TYR 0.014 0.001 TYR B 299 ARG 0.002 0.000 ARG A 589 ********************** 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 155 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.599 Fit side-chains REVERT: A 581 MET cc_start: 0.8194 (mmm) cc_final: 0.7533 (mmm) REVERT: A 597 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 634 MET cc_start: 0.9115 (mmm) cc_final: 0.8535 (mmm) REVERT: A 662 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7612 (t80) REVERT: B 55 MET cc_start: 0.8965 (mmp) cc_final: 0.8734 (mmp) REVERT: C 49 MET cc_start: 0.8432 (ppp) cc_final: 0.8015 (ppp) REVERT: C 286 MET cc_start: 0.8471 (mmp) cc_final: 0.8039 (tpp) REVERT: E 49 MET cc_start: 0.8295 (ttm) cc_final: 0.7781 (tmm) REVERT: E 185 GLN cc_start: 0.9006 (pm20) cc_final: 0.8684 (pm20) REVERT: E 190 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: D 213 MET cc_start: 0.8432 (mtm) cc_final: 0.7983 (mtm) REVERT: D 229 GLN cc_start: 0.8523 (tp40) cc_final: 0.8197 (tp40) REVERT: F 414 HIS cc_start: 0.8142 (m90) cc_final: 0.7807 (m90) REVERT: F 456 THR cc_start: 0.9328 (m) cc_final: 0.9080 (p) outliers start: 17 outliers final: 13 residues processed: 146 average time/residue: 0.2294 time to fit residues: 53.0059 Evaluate side-chains 145 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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** D 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.054839 restraints weight = 47987.120| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.50 r_work: 0.2886 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15199 Z= 0.175 Angle : 0.541 8.576 20657 Z= 0.269 Chirality : 0.041 0.358 2387 Planarity : 0.003 0.045 2536 Dihedral : 5.641 63.536 2453 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 1.07 % Allowed : 12.82 % 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: 1.03 (0.21), residues: 1764 helix: 2.39 (0.22), residues: 591 sheet: 0.03 (0.24), residues: 454 loop : -0.26 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 237 HIS 0.005 0.001 HIS D 110 PHE 0.018 0.001 PHE C 293 TYR 0.015 0.001 TYR B 299 ARG 0.003 0.000 ARG F 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2709.82 seconds wall clock time: 50 minutes 9.13 seconds (3009.13 seconds total)