Starting phenix.real_space_refine on Thu Mar 14 16:36:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/03_2024/6pqr_20452.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/03_2024/6pqr_20452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/03_2024/6pqr_20452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/03_2024/6pqr_20452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/03_2024/6pqr_20452.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/03_2024/6pqr_20452.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 2 6.06 5 P 88 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5612 2.51 5 N 1592 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 276": "NH1" <-> "NH2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 349": "OD1" <-> "OD2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ASP 399": "OD1" <-> "OD2" Residue "D ASP 416": "OD1" <-> "OD2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ARG 437": "NH1" <-> "NH2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 445": "NH1" <-> "NH2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D ASP 481": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9266 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3728 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "C" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3728 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 1, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 1, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1629 SG CYS A 240 77.598 110.856 39.273 1.00166.71 S ATOM 1655 SG CYS A 243 80.541 111.292 41.321 1.00170.90 S ATOM 6259 SG CYS D 240 25.377 15.136 39.255 1.00167.58 S ATOM 6285 SG CYS D 243 22.435 14.693 41.303 1.00171.67 S Time building chain proxies: 5.33, per 1000 atoms: 0.58 Number of scatterers: 9266 At special positions: 0 Unit cell: (103.95, 127.05, 91.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 2 19.00 S 34 16.00 P 88 15.00 Mg 2 11.99 O 1934 8.00 N 1592 7.00 C 5612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 240 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 413 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 408 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 243 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 240 " Number of angles added : 4 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 51.7% alpha, 15.8% beta 34 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.619A pdb=" N LEU A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.621A pdb=" N THR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.618A pdb=" N GLN A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.069A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 202 removed outlier: 3.547A pdb=" N VAL A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 289 removed outlier: 3.885A pdb=" N MET A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 321 Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.507A pdb=" N ARG A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.621A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 396 removed outlier: 3.522A pdb=" N GLU A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.585A pdb=" N LEU A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.868A pdb=" N ILE A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.735A pdb=" N ILE A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.797A pdb=" N VAL A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 494' Processing helix chain 'D' and resid 25 through 36 removed outlier: 3.619A pdb=" N LEU D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.623A pdb=" N THR D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.612A pdb=" N GLN D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 105 Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.070A pdb=" N TYR D 174 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.547A pdb=" N VAL D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 231 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 276 through 289 removed outlier: 3.884A pdb=" N MET D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 321 Processing helix chain 'D' and resid 337 through 347 removed outlier: 4.507A pdb=" N ARG D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 358 through 373 removed outlier: 3.620A pdb=" N ILE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 396 removed outlier: 3.522A pdb=" N GLU D 385 " --> pdb=" O PRO D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 413 removed outlier: 3.585A pdb=" N LEU D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.868A pdb=" N ILE D 417 " --> pdb=" O HIS D 413 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 447 Processing helix chain 'D' and resid 453 through 468 removed outlier: 3.734A pdb=" N ILE D 467 " --> pdb=" O ASN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 494 removed outlier: 3.796A pdb=" N VAL D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 489 through 494' Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 151 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 179 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 165 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 156 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 151 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 179 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE A 147 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA A 127 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR A 149 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP A 125 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A 151 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLY A 123 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS A 121 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N LEU A 116 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N LEU A 218 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LEU A 118 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N MET A 220 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N SER A 120 " --> pdb=" O MET A 220 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N MET A 222 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP A 122 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.261A pdb=" N ILE A 377 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL D 178 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 151 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 179 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU D 154 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL D 165 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 156 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL D 178 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 151 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 179 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE D 147 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA D 127 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR D 149 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP D 125 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU D 151 " --> pdb=" O GLY D 123 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY D 123 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS D 121 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N LEU D 116 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N LEU D 218 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LEU D 118 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N MET D 220 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N SER D 120 " --> pdb=" O MET D 220 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N MET D 222 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP D 122 " --> pdb=" O MET D 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 377 through 378 removed outlier: 4.261A pdb=" N ILE D 377 " --> pdb=" O GLN D 497 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2078 1.33 - 1.45: 2347 1.45 - 1.57: 4965 1.57 - 1.69: 172 1.69 - 1.81: 52 Bond restraints: 9614 Sorted by residual: bond pdb=" CG ARG A 450 " pdb=" CD ARG A 450 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.81e+00 bond pdb=" CG ARG D 450 " pdb=" CD ARG D 450 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.80e+00 bond pdb=" CA PHE D 147 " pdb=" CB PHE D 147 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.53e-02 4.27e+03 3.70e+00 bond pdb=" CA PHE A 147 " pdb=" CB PHE A 147 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.53e-02 4.27e+03 3.59e+00 bond pdb=" CB ARG D 450 " pdb=" CG ARG D 450 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 ... (remaining 9609 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.37: 498 105.37 - 112.53: 5251 112.53 - 119.69: 3275 119.69 - 126.85: 4011 126.85 - 134.01: 319 Bond angle restraints: 13354 Sorted by residual: angle pdb=" C GLU D 103 " pdb=" N THR D 104 " pdb=" CA THR D 104 " ideal model delta sigma weight residual 122.24 115.40 6.84 1.57e+00 4.06e-01 1.90e+01 angle pdb=" C GLU A 103 " pdb=" N THR A 104 " pdb=" CA THR A 104 " ideal model delta sigma weight residual 122.24 115.43 6.81 1.57e+00 4.06e-01 1.88e+01 angle pdb=" C GLU D 502 " pdb=" N ALA D 503 " pdb=" CA ALA D 503 " ideal model delta sigma weight residual 122.59 117.91 4.68 1.11e+00 8.12e-01 1.78e+01 angle pdb=" C GLU A 502 " pdb=" N ALA A 503 " pdb=" CA ALA A 503 " ideal model delta sigma weight residual 122.59 117.94 4.65 1.11e+00 8.12e-01 1.75e+01 angle pdb=" C ALA D 234 " pdb=" N LYS D 235 " pdb=" CA LYS D 235 " ideal model delta sigma weight residual 120.82 126.88 -6.06 1.50e+00 4.44e-01 1.63e+01 ... (remaining 13349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 4336 16.84 - 33.68: 716 33.68 - 50.52: 394 50.52 - 67.37: 154 67.37 - 84.21: 14 Dihedral angle restraints: 5614 sinusoidal: 2862 harmonic: 2752 Sorted by residual: dihedral pdb=" CA ASP D 326 " pdb=" C ASP D 326 " pdb=" N ILE D 327 " pdb=" CA ILE D 327 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ASP A 326 " pdb=" C ASP A 326 " pdb=" N ILE A 327 " pdb=" CA ILE A 327 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ALA A 234 " pdb=" C ALA A 234 " pdb=" N LYS A 235 " pdb=" CA LYS A 235 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 5611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 869 0.037 - 0.075: 487 0.075 - 0.112: 126 0.112 - 0.149: 27 0.149 - 0.186: 13 Chirality restraints: 1522 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CB ILE D 105 " pdb=" CA ILE D 105 " pdb=" CG1 ILE D 105 " pdb=" CG2 ILE D 105 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CG LEU A 270 " pdb=" CB LEU A 270 " pdb=" CD1 LEU A 270 " pdb=" CD2 LEU A 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 1519 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 450 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C ARG D 450 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG D 450 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS D 451 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 450 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C ARG A 450 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG A 450 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 451 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 31 " -0.019 2.00e-02 2.50e+03 8.23e-03 1.86e+00 pdb=" N9 DA B 31 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA B 31 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA B 31 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA B 31 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA B 31 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA B 31 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA B 31 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA B 31 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA B 31 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA B 31 " 0.007 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 462 2.69 - 3.30: 10606 3.30 - 3.92: 18688 3.92 - 4.53: 24093 4.53 - 5.14: 36038 Nonbonded interactions: 89887 Sorted by model distance: nonbonded pdb=" OD1 ASP A 125 " pdb="MG MG A 601 " model vdw 2.081 2.170 nonbonded pdb=" OD1 ASP D 125 " pdb="MG MG D 601 " model vdw 2.081 2.170 nonbonded pdb=" OD2 ASP A 224 " pdb="MG MG A 601 " model vdw 2.098 2.170 nonbonded pdb=" OD2 ASP D 224 " pdb="MG MG D 601 " model vdw 2.098 2.170 nonbonded pdb=" OG1 THR D 186 " pdb=" OD1 ASP D 188 " model vdw 2.201 2.440 ... (remaining 89882 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' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.030 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.970 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.009 0.059 9614 Z= 0.550 Angle : 0.839 6.844 13354 Z= 0.505 Chirality : 0.049 0.186 1522 Planarity : 0.004 0.033 1380 Dihedral : 22.102 84.207 3822 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.24 % Allowed : 11.59 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.38 (0.23), residues: 920 helix: -2.20 (0.19), residues: 452 sheet: -0.96 (0.57), residues: 60 loop : -2.38 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 400 HIS 0.008 0.002 HIS A 413 PHE 0.023 0.002 PHE A 102 TYR 0.011 0.002 TYR A 394 ARG 0.007 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 HIS cc_start: 0.7547 (m90) cc_final: 0.7150 (m170) REVERT: A 344 PHE cc_start: 0.7881 (t80) cc_final: 0.7551 (t80) REVERT: A 417 ILE cc_start: 0.7852 (mm) cc_final: 0.7599 (mt) REVERT: D 285 HIS cc_start: 0.7553 (m90) cc_final: 0.7164 (m170) REVERT: D 344 PHE cc_start: 0.7873 (t80) cc_final: 0.7467 (t80) outliers start: 2 outliers final: 2 residues processed: 115 average time/residue: 0.2350 time to fit residues: 36.6906 Evaluate side-chains 80 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.0000 chunk 90 optimal weight: 1.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 314 GLN A 421 ASN A 448 HIS D 66 GLN D 314 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN D 448 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9614 Z= 0.197 Angle : 0.600 7.757 13354 Z= 0.334 Chirality : 0.041 0.208 1522 Planarity : 0.004 0.035 1380 Dihedral : 24.936 70.893 1972 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.17 % Allowed : 16.91 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.86 (0.25), residues: 920 helix: -0.75 (0.23), residues: 442 sheet: -0.14 (0.59), residues: 60 loop : -1.90 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 41 HIS 0.004 0.001 HIS A 408 PHE 0.014 0.002 PHE A 268 TYR 0.012 0.001 TYR A 241 ARG 0.008 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7980 (ttp) cc_final: 0.7416 (ttp) REVERT: A 285 HIS cc_start: 0.7653 (m90) cc_final: 0.7245 (m-70) REVERT: A 417 ILE cc_start: 0.7826 (mm) cc_final: 0.7568 (mt) REVERT: D 281 GLU cc_start: 0.7458 (pp20) cc_final: 0.7239 (pp20) REVERT: D 285 HIS cc_start: 0.7674 (m90) cc_final: 0.7282 (m-70) outliers start: 18 outliers final: 5 residues processed: 116 average time/residue: 0.1888 time to fit residues: 31.6056 Evaluate side-chains 96 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9614 Z= 0.203 Angle : 0.568 8.198 13354 Z= 0.314 Chirality : 0.040 0.197 1522 Planarity : 0.003 0.032 1380 Dihedral : 24.688 68.316 1972 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.05 % Allowed : 19.20 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.26), residues: 920 helix: -0.38 (0.23), residues: 458 sheet: 0.09 (0.62), residues: 60 loop : -1.88 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 400 HIS 0.004 0.001 HIS D 413 PHE 0.010 0.002 PHE D 268 TYR 0.010 0.001 TYR A 241 ARG 0.003 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7961 (ttp) cc_final: 0.7622 (ttp) REVERT: A 417 ILE cc_start: 0.7680 (mm) cc_final: 0.7434 (mt) REVERT: D 285 HIS cc_start: 0.7654 (m90) cc_final: 0.7395 (m170) REVERT: D 344 PHE cc_start: 0.8098 (t80) cc_final: 0.7861 (t80) outliers start: 17 outliers final: 9 residues processed: 115 average time/residue: 0.1841 time to fit residues: 31.0101 Evaluate side-chains 103 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 492 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN D 314 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9614 Z= 0.248 Angle : 0.570 7.797 13354 Z= 0.316 Chirality : 0.041 0.194 1522 Planarity : 0.003 0.042 1380 Dihedral : 24.590 66.649 1972 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.66 % Allowed : 20.53 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.26), residues: 920 helix: -0.11 (0.23), residues: 458 sheet: -0.17 (0.59), residues: 64 loop : -1.88 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 400 HIS 0.002 0.001 HIS D 408 PHE 0.019 0.002 PHE A 345 TYR 0.014 0.001 TYR A 488 ARG 0.005 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7926 (ttp) cc_final: 0.7609 (ttp) REVERT: A 344 PHE cc_start: 0.8058 (t80) cc_final: 0.7767 (t80) REVERT: A 402 TYR cc_start: 0.6470 (m-80) cc_final: 0.5843 (p90) REVERT: A 403 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6194 (mmt) REVERT: A 417 ILE cc_start: 0.7672 (mm) cc_final: 0.7426 (mt) REVERT: D 344 PHE cc_start: 0.8088 (t80) cc_final: 0.7791 (t80) outliers start: 22 outliers final: 13 residues processed: 115 average time/residue: 0.1999 time to fit residues: 32.7246 Evaluate side-chains 107 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 278 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9614 Z= 0.213 Angle : 0.550 6.743 13354 Z= 0.304 Chirality : 0.039 0.164 1522 Planarity : 0.003 0.032 1380 Dihedral : 24.450 71.272 1972 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.17 % Allowed : 22.22 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.26), residues: 920 helix: 0.04 (0.23), residues: 458 sheet: 0.08 (0.60), residues: 64 loop : -1.92 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 400 HIS 0.003 0.001 HIS A 413 PHE 0.011 0.001 PHE A 345 TYR 0.008 0.001 TYR A 488 ARG 0.006 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7943 (ttp) cc_final: 0.6886 (tpt) REVERT: A 344 PHE cc_start: 0.8020 (t80) cc_final: 0.7817 (t80) REVERT: A 402 TYR cc_start: 0.6520 (m-80) cc_final: 0.5846 (p90) REVERT: A 403 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6226 (mmt) REVERT: A 417 ILE cc_start: 0.7654 (mm) cc_final: 0.7398 (mt) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.1908 time to fit residues: 30.2993 Evaluate side-chains 107 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 430 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 93 optimal weight: 0.0570 chunk 10 optimal weight: 0.1980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN D 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9614 Z= 0.160 Angle : 0.518 5.959 13354 Z= 0.290 Chirality : 0.037 0.157 1522 Planarity : 0.003 0.030 1380 Dihedral : 24.182 73.725 1972 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.54 % Allowed : 22.95 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 920 helix: 0.25 (0.23), residues: 458 sheet: 0.65 (0.64), residues: 64 loop : -1.92 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 400 HIS 0.003 0.001 HIS D 413 PHE 0.016 0.001 PHE D 345 TYR 0.016 0.001 TYR D 488 ARG 0.003 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7833 (ttp) cc_final: 0.7044 (tpt) REVERT: A 357 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6519 (mm) REVERT: A 402 TYR cc_start: 0.6536 (m-80) cc_final: 0.5844 (p90) REVERT: A 417 ILE cc_start: 0.7574 (mm) cc_final: 0.7320 (mt) REVERT: D 280 MET cc_start: 0.7183 (ttp) cc_final: 0.6374 (tpt) REVERT: D 357 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6670 (mm) REVERT: D 402 TYR cc_start: 0.6349 (m-80) cc_final: 0.5759 (p90) REVERT: D 403 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6318 (mmt) outliers start: 21 outliers final: 11 residues processed: 110 average time/residue: 0.2107 time to fit residues: 33.3873 Evaluate side-chains 105 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 403 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 chunk 44 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9614 Z= 0.210 Angle : 0.539 6.122 13354 Z= 0.298 Chirality : 0.038 0.170 1522 Planarity : 0.003 0.030 1380 Dihedral : 24.155 73.535 1972 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.14 % Allowed : 22.71 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 920 helix: 0.40 (0.24), residues: 458 sheet: 0.69 (0.64), residues: 64 loop : -1.89 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 400 HIS 0.002 0.001 HIS D 408 PHE 0.022 0.002 PHE A 345 TYR 0.012 0.001 TYR A 488 ARG 0.004 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7787 (ttp) cc_final: 0.7126 (tpt) REVERT: A 357 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6514 (mm) REVERT: A 402 TYR cc_start: 0.6451 (m-80) cc_final: 0.5774 (p90) REVERT: A 403 MET cc_start: 0.6183 (tpp) cc_final: 0.5717 (tpp) REVERT: A 417 ILE cc_start: 0.7563 (mm) cc_final: 0.7322 (mt) REVERT: D 357 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6644 (mm) REVERT: D 402 TYR cc_start: 0.6354 (m-80) cc_final: 0.5764 (p90) REVERT: D 403 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6288 (mmt) outliers start: 26 outliers final: 14 residues processed: 106 average time/residue: 0.2005 time to fit residues: 30.8990 Evaluate side-chains 102 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0030 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9614 Z= 0.244 Angle : 0.552 6.117 13354 Z= 0.306 Chirality : 0.039 0.160 1522 Planarity : 0.003 0.031 1380 Dihedral : 24.117 76.342 1972 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.54 % Allowed : 23.79 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 920 helix: 0.40 (0.24), residues: 458 sheet: -0.17 (0.72), residues: 48 loop : -1.91 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 400 HIS 0.002 0.001 HIS D 408 PHE 0.011 0.001 PHE A 345 TYR 0.011 0.001 TYR A 488 ARG 0.003 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 280 MET cc_start: 0.7821 (ttp) cc_final: 0.7197 (tpt) REVERT: A 357 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6565 (mm) REVERT: A 402 TYR cc_start: 0.6491 (m-80) cc_final: 0.5806 (p90) REVERT: A 403 MET cc_start: 0.6357 (tpp) cc_final: 0.5935 (tpp) REVERT: A 417 ILE cc_start: 0.7557 (mm) cc_final: 0.7319 (mt) REVERT: D 226 LYS cc_start: 0.8497 (ptpt) cc_final: 0.8118 (mttm) REVERT: D 280 MET cc_start: 0.7375 (ttp) cc_final: 0.6656 (tpt) REVERT: D 345 PHE cc_start: 0.7944 (m-80) cc_final: 0.7632 (m-80) REVERT: D 357 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6650 (mm) REVERT: D 392 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7290 (mt-10) REVERT: D 402 TYR cc_start: 0.6376 (m-80) cc_final: 0.5783 (p90) REVERT: D 403 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6357 (tpp) outliers start: 21 outliers final: 14 residues processed: 102 average time/residue: 0.1896 time to fit residues: 28.0205 Evaluate side-chains 103 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 403 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 27 optimal weight: 0.1980 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7701 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9614 Z= 0.167 Angle : 0.514 5.946 13354 Z= 0.287 Chirality : 0.037 0.155 1522 Planarity : 0.003 0.029 1380 Dihedral : 23.891 79.751 1972 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.29 % Allowed : 24.03 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 920 helix: 0.51 (0.24), residues: 460 sheet: 0.03 (0.74), residues: 48 loop : -1.87 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 400 HIS 0.003 0.001 HIS D 413 PHE 0.014 0.001 PHE A 489 TYR 0.009 0.001 TYR A 488 ARG 0.002 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7975 (tm-30) REVERT: A 280 MET cc_start: 0.7746 (ttp) cc_final: 0.7188 (tpt) REVERT: A 357 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6509 (mm) REVERT: A 402 TYR cc_start: 0.6603 (m-80) cc_final: 0.5850 (p90) REVERT: A 403 MET cc_start: 0.6307 (tpp) cc_final: 0.5852 (tpp) REVERT: A 417 ILE cc_start: 0.7525 (mm) cc_final: 0.7286 (mt) REVERT: D 226 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8123 (mttm) REVERT: D 280 MET cc_start: 0.7285 (ttp) cc_final: 0.6583 (tpt) REVERT: D 345 PHE cc_start: 0.7942 (m-80) cc_final: 0.7576 (m-80) REVERT: D 357 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6715 (mm) REVERT: D 392 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7254 (mt-10) REVERT: D 402 TYR cc_start: 0.6520 (m-80) cc_final: 0.5834 (p90) REVERT: D 403 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6299 (tpp) outliers start: 19 outliers final: 12 residues processed: 102 average time/residue: 0.2066 time to fit residues: 30.1397 Evaluate side-chains 102 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 403 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9614 Z= 0.277 Angle : 0.562 6.098 13354 Z= 0.310 Chirality : 0.039 0.159 1522 Planarity : 0.003 0.031 1380 Dihedral : 23.982 78.025 1972 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.17 % Allowed : 24.64 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 920 helix: 0.44 (0.24), residues: 462 sheet: -0.18 (0.74), residues: 48 loop : -1.86 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 400 HIS 0.003 0.001 HIS D 408 PHE 0.014 0.002 PHE A 345 TYR 0.011 0.001 TYR A 488 ARG 0.005 0.000 ARG D 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7809 (ttp) cc_final: 0.7158 (tpt) REVERT: A 357 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6563 (mm) REVERT: A 402 TYR cc_start: 0.6568 (m-80) cc_final: 0.5877 (p90) REVERT: A 403 MET cc_start: 0.6454 (tpp) cc_final: 0.6019 (tpp) REVERT: A 417 ILE cc_start: 0.7591 (mm) cc_final: 0.7375 (mt) REVERT: D 226 LYS cc_start: 0.8497 (ptpt) cc_final: 0.8153 (mttm) REVERT: D 280 MET cc_start: 0.7327 (ttp) cc_final: 0.6587 (tpt) REVERT: D 345 PHE cc_start: 0.7987 (m-80) cc_final: 0.7605 (m-80) REVERT: D 357 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6712 (mm) REVERT: D 402 TYR cc_start: 0.6452 (m-80) cc_final: 0.5861 (p90) REVERT: D 403 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6324 (tpp) outliers start: 18 outliers final: 12 residues processed: 98 average time/residue: 0.1896 time to fit residues: 27.2260 Evaluate side-chains 98 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 403 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 0.0020 chunk 79 optimal weight: 0.0050 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4802 ------------------------------------------------------------------------------- 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 = 0.4536 r_free = 0.4536 target = 0.194865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.142157 restraints weight = 14268.954| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.74 r_work: 0.3710 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9614 Z= 0.164 Angle : 0.524 6.049 13354 Z= 0.292 Chirality : 0.037 0.153 1522 Planarity : 0.003 0.028 1380 Dihedral : 23.836 81.906 1972 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.69 % Allowed : 25.36 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.27), residues: 920 helix: 0.53 (0.24), residues: 460 sheet: 0.03 (0.75), residues: 48 loop : -1.82 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.002 0.001 HIS D 413 PHE 0.015 0.001 PHE A 489 TYR 0.008 0.001 TYR D 488 ARG 0.003 0.000 ARG D 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1879.41 seconds wall clock time: 34 minutes 48.16 seconds (2088.16 seconds total)