Starting phenix.real_space_refine on Wed Sep 25 02:01:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/09_2024/6pqr_20452.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/09_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_20452/09_2024/6pqr_20452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/09_2024/6pqr_20452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/09_2024/6pqr_20452.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqr_20452/09_2024/6pqr_20452.cif" } 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. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.51, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 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: 2.72 Conformation dependent library (CDL) restraints added in 948.0 milliseconds 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: 3.56 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: 3.23 Time building geometry restraints manager: 3.13 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: 0.00 - 1.37: 12178 1.37 - 2.74: 1003 2.74 - 4.11: 127 4.11 - 5.48: 38 5.48 - 6.84: 8 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 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 3.050 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.410 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- 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 : 0.955 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: 0.2342 time to fit residues: 36.6974 Evaluate side-chains 80 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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: 0.8980 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 314 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN D 448 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9614 Z= 0.211 Angle : 0.615 8.064 13354 Z= 0.342 Chirality : 0.042 0.215 1522 Planarity : 0.004 0.033 1380 Dihedral : 24.973 71.021 1972 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.93 % Allowed : 15.94 % Favored : 82.13 % 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: -1.97 (0.25), residues: 920 helix: -0.87 (0.22), residues: 442 sheet: -0.33 (0.59), residues: 60 loop : -1.88 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 400 HIS 0.005 0.001 HIS D 413 PHE 0.015 0.002 PHE A 268 TYR 0.012 0.002 TYR D 241 ARG 0.005 0.001 ARG D 343 *********************** 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 123 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.8026 (ttp) cc_final: 0.7420 (ttp) REVERT: A 281 GLU cc_start: 0.7368 (pp20) cc_final: 0.7158 (pp20) REVERT: A 285 HIS cc_start: 0.7624 (m90) cc_final: 0.7202 (m-70) REVERT: A 417 ILE cc_start: 0.7827 (mm) cc_final: 0.7576 (mt) REVERT: D 281 GLU cc_start: 0.7435 (pp20) cc_final: 0.7201 (pp20) REVERT: D 285 HIS cc_start: 0.7508 (m90) cc_final: 0.7125 (m-70) outliers start: 16 outliers final: 4 residues processed: 113 average time/residue: 0.1922 time to fit residues: 31.5315 Evaluate side-chains 94 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7761 moved from start: 0.2027 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= 0.204 Angle : 0.577 8.652 13354 Z= 0.319 Chirality : 0.040 0.208 1522 Planarity : 0.004 0.032 1380 Dihedral : 24.685 68.245 1972 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.81 % Allowed : 17.87 % Favored : 80.31 % 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: -1.47 (0.26), residues: 920 helix: -0.36 (0.22), residues: 444 sheet: -0.02 (0.63), residues: 60 loop : -1.77 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 400 HIS 0.005 0.001 HIS D 413 PHE 0.009 0.002 PHE A 268 TYR 0.009 0.001 TYR A 241 ARG 0.002 0.000 ARG D 342 *********************** 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 122 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7939 (ttp) cc_final: 0.7302 (ttp) REVERT: A 285 HIS cc_start: 0.7729 (m90) cc_final: 0.7471 (m170) REVERT: A 344 PHE cc_start: 0.8165 (t80) cc_final: 0.7964 (t80) REVERT: A 417 ILE cc_start: 0.7649 (mm) cc_final: 0.7420 (mt) REVERT: D 280 MET cc_start: 0.7298 (ttp) cc_final: 0.6291 (tpt) REVERT: D 285 HIS cc_start: 0.7678 (m90) cc_final: 0.7424 (m170) REVERT: D 344 PHE cc_start: 0.8088 (t80) cc_final: 0.7342 (t80) outliers start: 15 outliers final: 7 residues processed: 118 average time/residue: 0.1841 time to fit residues: 31.6894 Evaluate side-chains 102 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 HIS ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9614 Z= 0.237 Angle : 0.578 8.648 13354 Z= 0.318 Chirality : 0.041 0.219 1522 Planarity : 0.004 0.032 1380 Dihedral : 24.573 66.294 1972 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 19.69 % Favored : 78.50 % 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: -1.32 (0.26), residues: 920 helix: -0.23 (0.22), residues: 458 sheet: 0.19 (0.63), residues: 60 loop : -1.77 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 400 HIS 0.002 0.001 HIS D 413 PHE 0.014 0.002 PHE D 345 TYR 0.013 0.001 TYR A 488 ARG 0.003 0.000 ARG D 364 *********************** 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 113 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: A 280 MET cc_start: 0.7947 (ttp) cc_final: 0.7700 (ttp) REVERT: A 281 GLU cc_start: 0.7511 (pp20) cc_final: 0.7297 (tm-30) REVERT: A 402 TYR cc_start: 0.6262 (m-80) cc_final: 0.5552 (p90) REVERT: A 417 ILE cc_start: 0.7632 (mm) cc_final: 0.7404 (mt) REVERT: D 226 LYS cc_start: 0.8543 (ptpt) cc_final: 0.8274 (mttm) outliers start: 15 outliers final: 8 residues processed: 107 average time/residue: 0.2099 time to fit residues: 33.0876 Evaluate side-chains 103 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 171 SER Chi-restraints excluded: chain A residue 185 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7752 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9614 Z= 0.201 Angle : 0.555 7.719 13354 Z= 0.308 Chirality : 0.040 0.192 1522 Planarity : 0.003 0.031 1380 Dihedral : 24.452 66.663 1972 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.66 % Allowed : 21.14 % Favored : 76.21 % 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: -1.15 (0.26), residues: 920 helix: -0.07 (0.22), residues: 460 sheet: 0.30 (0.65), residues: 60 loop : -1.74 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 41 HIS 0.002 0.001 HIS D 413 PHE 0.021 0.002 PHE D 345 TYR 0.011 0.001 TYR D 73 ARG 0.004 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 124 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: A 226 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8297 (mttm) REVERT: A 280 MET cc_start: 0.7995 (ttp) cc_final: 0.6869 (tpt) REVERT: A 402 TYR cc_start: 0.6256 (m-80) cc_final: 0.5533 (p90) REVERT: A 417 ILE cc_start: 0.7589 (mm) cc_final: 0.7351 (mt) REVERT: D 226 LYS cc_start: 0.8531 (ptpt) cc_final: 0.8295 (mttm) REVERT: D 280 MET cc_start: 0.7401 (ttp) cc_final: 0.6491 (tpt) outliers start: 22 outliers final: 6 residues processed: 115 average time/residue: 0.1859 time to fit residues: 30.9909 Evaluate side-chains 103 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 185 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 96 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 314 GLN D 91 GLN D 336 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2760 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= 0.181 Angle : 0.540 5.817 13354 Z= 0.300 Chirality : 0.038 0.160 1522 Planarity : 0.003 0.030 1380 Dihedral : 24.265 71.512 1972 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.05 % Allowed : 22.46 % Favored : 75.48 % 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: -0.94 (0.27), residues: 920 helix: 0.11 (0.23), residues: 460 sheet: 0.35 (0.64), residues: 64 loop : -1.65 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 41 HIS 0.003 0.001 HIS D 413 PHE 0.013 0.001 PHE D 180 TYR 0.006 0.001 TYR A 62 ARG 0.005 0.000 ARG D 364 *********************** 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 110 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: A 280 MET cc_start: 0.7758 (ttp) cc_final: 0.7144 (tpt) REVERT: A 357 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6593 (mm) REVERT: A 402 TYR cc_start: 0.6354 (m-80) cc_final: 0.5592 (p90) REVERT: A 417 ILE cc_start: 0.7530 (mm) cc_final: 0.7307 (mt) REVERT: A 442 ARG cc_start: 0.8453 (mtm-85) cc_final: 0.8118 (mtm-85) REVERT: D 357 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6649 (mm) outliers start: 17 outliers final: 9 residues processed: 104 average time/residue: 0.2040 time to fit residues: 30.2868 Evaluate side-chains 102 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 185 GLU 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 357 LEU Chi-restraints excluded: chain D residue 367 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0270 chunk 70 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.0060 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4454 ------------------------------------------------------------------------------- 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: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9614 Z= 0.162 Angle : 0.527 5.854 13354 Z= 0.294 Chirality : 0.038 0.159 1522 Planarity : 0.003 0.041 1380 Dihedral : 24.131 73.025 1972 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.93 % Allowed : 22.46 % 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: -0.84 (0.27), residues: 920 helix: 0.25 (0.23), residues: 460 sheet: 0.46 (0.66), residues: 64 loop : -1.68 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 295 HIS 0.002 0.000 HIS D 413 PHE 0.012 0.001 PHE A 489 TYR 0.021 0.001 TYR D 73 ARG 0.007 0.001 ARG A 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 108 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.916 Fit side-chains REVERT: A 185 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: A 280 MET cc_start: 0.7838 (ttp) cc_final: 0.7213 (tpt) REVERT: A 357 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6492 (mm) REVERT: A 392 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 402 TYR cc_start: 0.6241 (m-80) cc_final: 0.5699 (p90) REVERT: A 417 ILE cc_start: 0.7398 (mm) cc_final: 0.7179 (mt) REVERT: A 442 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8103 (mtm-85) REVERT: D 280 MET cc_start: 0.7271 (ttp) cc_final: 0.6601 (tpt) REVERT: D 357 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6578 (mm) REVERT: D 392 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7336 (mt-10) outliers start: 16 outliers final: 9 residues processed: 104 average time/residue: 0.2071 time to fit residues: 30.9274 Evaluate side-chains 98 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 185 GLU 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 96 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.0792 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9614 Z= 0.205 Angle : 0.551 7.056 13354 Z= 0.303 Chirality : 0.038 0.161 1522 Planarity : 0.003 0.029 1380 Dihedral : 24.085 73.497 1972 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.69 % Allowed : 22.58 % Favored : 75.72 % 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: -0.91 (0.27), residues: 920 helix: 0.29 (0.23), residues: 460 sheet: -0.06 (0.74), residues: 48 loop : -1.70 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 400 HIS 0.002 0.001 HIS A 413 PHE 0.013 0.001 PHE D 489 TYR 0.021 0.001 TYR D 488 ARG 0.003 0.000 ARG D 364 *********************** 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 102 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.918 Fit side-chains REVERT: A 185 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: A 280 MET cc_start: 0.7838 (ttp) cc_final: 0.7231 (tpt) REVERT: A 357 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6409 (mm) REVERT: A 364 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6766 (ptm160) REVERT: A 392 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 402 TYR cc_start: 0.6140 (m-80) cc_final: 0.5703 (p90) REVERT: A 403 MET cc_start: 0.7213 (mmt) cc_final: 0.6780 (mmm) REVERT: A 417 ILE cc_start: 0.7400 (mm) cc_final: 0.7191 (mt) REVERT: A 442 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8110 (mtm-85) REVERT: D 280 MET cc_start: 0.7357 (ttp) cc_final: 0.6467 (tpt) REVERT: D 357 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6698 (mm) REVERT: D 392 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7393 (mt-10) outliers start: 14 outliers final: 8 residues processed: 96 average time/residue: 0.2043 time to fit residues: 28.0719 Evaluate side-chains 99 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 185 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 ARG 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 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.0070 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9614 Z= 0.161 Angle : 0.540 10.943 13354 Z= 0.296 Chirality : 0.037 0.164 1522 Planarity : 0.003 0.028 1380 Dihedral : 23.863 75.851 1972 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.81 % Allowed : 22.58 % 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: -0.76 (0.27), residues: 920 helix: 0.41 (0.24), residues: 460 sheet: 0.22 (0.76), residues: 48 loop : -1.66 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 122 HIS 0.002 0.001 HIS A 413 PHE 0.014 0.001 PHE D 489 TYR 0.016 0.001 TYR A 488 ARG 0.003 0.000 ARG A 343 *********************** 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 101 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.662 Fit side-chains REVERT: A 280 MET cc_start: 0.7763 (ttp) cc_final: 0.7350 (tpt) REVERT: A 357 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6622 (mm) REVERT: A 442 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.7933 (mtt-85) REVERT: D 261 ILE cc_start: 0.3160 (OUTLIER) cc_final: 0.2828 (pt) REVERT: D 280 MET cc_start: 0.7351 (ttp) cc_final: 0.6607 (tpt) REVERT: D 357 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6751 (mm) REVERT: D 392 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7454 (mt-10) REVERT: D 403 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6216 (mmt) outliers start: 15 outliers final: 6 residues processed: 95 average time/residue: 0.1590 time to fit residues: 21.4723 Evaluate side-chains 92 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 171 SER 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 171 SER Chi-restraints excluded: chain D residue 261 ILE 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: 0.8980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 79 optimal weight: 0.0040 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 0.0570 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5110 ------------------------------------------------------------------------------- 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: 0.7670 moved from start: 0.3569 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= 0.161 Angle : 0.521 5.567 13354 Z= 0.289 Chirality : 0.037 0.159 1522 Planarity : 0.003 0.030 1380 Dihedral : 23.838 75.486 1970 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.33 % Allowed : 23.43 % Favored : 75.24 % 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: -0.69 (0.27), residues: 920 helix: 0.48 (0.24), residues: 460 sheet: 0.27 (0.78), residues: 48 loop : -1.65 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 295 HIS 0.003 0.000 HIS A 413 PHE 0.013 0.001 PHE A 489 TYR 0.009 0.001 TYR D 488 ARG 0.003 0.000 ARG D 106 ********************** 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 93 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.880 Fit side-chains REVERT: A 280 MET cc_start: 0.7815 (ttp) cc_final: 0.7334 (tpt) REVERT: A 357 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6669 (mm) REVERT: A 392 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7592 (mt-10) REVERT: A 403 MET cc_start: 0.6779 (mmt) cc_final: 0.6381 (mmt) REVERT: A 442 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7916 (mtt-85) REVERT: D 261 ILE cc_start: 0.3150 (OUTLIER) cc_final: 0.2840 (pt) REVERT: D 357 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6678 (mm) REVERT: D 392 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7473 (mt-10) outliers start: 11 outliers final: 5 residues processed: 88 average time/residue: 0.2049 time to fit residues: 25.7140 Evaluate side-chains 88 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.195599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.142522 restraints weight = 14420.956| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.78 r_work: 0.3714 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3592 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= 0.189 Angle : 0.533 5.728 13354 Z= 0.294 Chirality : 0.038 0.159 1522 Planarity : 0.003 0.030 1380 Dihedral : 23.815 76.804 1970 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.21 % Allowed : 23.91 % Favored : 74.88 % 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: -0.66 (0.26), residues: 920 helix: 0.49 (0.23), residues: 460 sheet: 0.28 (0.77), residues: 48 loop : -1.61 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 122 HIS 0.002 0.001 HIS D 413 PHE 0.013 0.001 PHE A 489 TYR 0.012 0.001 TYR D 488 ARG 0.003 0.000 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.51 seconds wall clock time: 38 minutes 24.50 seconds (2304.50 seconds total)