Starting phenix.real_space_refine on Thu Mar 13 21:54:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqr_20452/03_2025/6pqr_20452.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqr_20452/03_2025/6pqr_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/cci-nas-00/data/ceres_data/6pqr_20452/03_2025/6pqr_20452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqr_20452/03_2025/6pqr_20452.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqr_20452/03_2025/6pqr_20452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqr_20452/03_2025/6pqr_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-5624/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: 5.93, per 1000 atoms: 0.64 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: 2.75 Conformation dependent library (CDL) restraints added in 900.8 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: 3.81 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: 4.11 Time building geometry restraints manager: 3.20 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'A' selection = chain 'D' } 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: 1.030 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.090 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.900 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: 0.2429 time to fit residues: 38.1323 Evaluate side-chains 80 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.183943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.128837 restraints weight = 14069.553| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.89 r_work: 0.3611 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7851 (ttp) cc_final: 0.7280 (ttp) REVERT: A 281 GLU cc_start: 0.7656 (pp20) cc_final: 0.7435 (pp20) REVERT: A 285 HIS cc_start: 0.7887 (m90) cc_final: 0.7448 (m-70) REVERT: A 344 PHE cc_start: 0.7795 (t80) cc_final: 0.7520 (t80) REVERT: D 220 MET cc_start: 0.8832 (ttp) cc_final: 0.8630 (ttp) REVERT: D 280 MET cc_start: 0.7335 (ttp) cc_final: 0.7127 (ttp) REVERT: D 281 GLU cc_start: 0.7702 (pp20) cc_final: 0.7470 (pp20) REVERT: D 285 HIS cc_start: 0.7783 (m90) cc_final: 0.7381 (m-70) REVERT: D 344 PHE cc_start: 0.7793 (t80) cc_final: 0.7574 (t80) outliers start: 16 outliers final: 4 residues processed: 113 average time/residue: 0.1857 time to fit residues: 30.4538 Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 87 optimal weight: 0.0370 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.191467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138834 restraints weight = 14358.372| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.80 r_work: 0.3662 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9614 Z= 0.179 Angle : 0.567 8.706 13354 Z= 0.313 Chirality : 0.040 0.212 1522 Planarity : 0.003 0.031 1380 Dihedral : 24.633 67.873 1972 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.81 % Allowed : 17.39 % Favored : 80.80 % 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: -1.41 (0.25), residues: 920 helix: -0.31 (0.22), residues: 444 sheet: 0.09 (0.63), residues: 60 loop : -1.77 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 400 HIS 0.004 0.001 HIS D 413 PHE 0.010 0.001 PHE D 180 TYR 0.011 0.001 TYR A 488 ARG 0.003 0.000 ARG D 364 *********************** 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 121 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7759 (ttp) cc_final: 0.7283 (ttp) REVERT: A 285 HIS cc_start: 0.7954 (m90) cc_final: 0.7702 (m170) REVERT: D 285 HIS cc_start: 0.7899 (m90) cc_final: 0.7661 (m170) outliers start: 15 outliers final: 7 residues processed: 118 average time/residue: 0.1999 time to fit residues: 34.0116 Evaluate side-chains 96 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 78 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.0870 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.187226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.132471 restraints weight = 14197.965| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.90 r_work: 0.3658 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9614 Z= 0.189 Angle : 0.553 8.000 13354 Z= 0.307 Chirality : 0.040 0.202 1522 Planarity : 0.003 0.030 1380 Dihedral : 24.521 65.970 1972 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.45 % Allowed : 19.69 % Favored : 78.86 % 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: -1.12 (0.26), residues: 920 helix: -0.05 (0.23), residues: 448 sheet: 0.36 (0.65), residues: 60 loop : -1.67 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.002 0.001 HIS D 413 PHE 0.012 0.001 PHE A 292 TYR 0.012 0.001 TYR A 488 ARG 0.004 0.000 ARG D 106 *********************** 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 107 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8265 (ptpt) cc_final: 0.7989 (mttm) REVERT: A 280 MET cc_start: 0.7705 (ttp) cc_final: 0.7345 (ttp) REVERT: A 281 GLU cc_start: 0.7803 (pp20) cc_final: 0.7601 (tm-30) REVERT: A 344 PHE cc_start: 0.8134 (t80) cc_final: 0.7696 (t80) REVERT: D 226 LYS cc_start: 0.8289 (ptpt) cc_final: 0.8010 (mttm) outliers start: 12 outliers final: 6 residues processed: 101 average time/residue: 0.2840 time to fit residues: 41.9665 Evaluate side-chains 100 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 66 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.180842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.124477 restraints weight = 14286.115| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.92 r_work: 0.3548 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9614 Z= 0.440 Angle : 0.671 7.612 13354 Z= 0.366 Chirality : 0.045 0.191 1522 Planarity : 0.004 0.036 1380 Dihedral : 24.684 75.174 1972 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.02 % Allowed : 20.53 % Favored : 76.45 % 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: -1.25 (0.26), residues: 920 helix: -0.11 (0.23), residues: 444 sheet: -0.08 (0.61), residues: 60 loop : -1.72 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 122 HIS 0.004 0.001 HIS D 447 PHE 0.026 0.002 PHE D 345 TYR 0.016 0.002 TYR D 73 ARG 0.006 0.001 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 114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7761 (ttp) cc_final: 0.7475 (ttp) REVERT: A 402 TYR cc_start: 0.6358 (m-80) cc_final: 0.5702 (p90) REVERT: D 185 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: D 226 LYS cc_start: 0.8324 (ptpt) cc_final: 0.8041 (mttm) REVERT: D 280 MET cc_start: 0.6972 (ttp) cc_final: 0.5950 (tpt) REVERT: D 402 TYR cc_start: 0.6161 (m-80) cc_final: 0.5517 (p90) REVERT: D 485 ARG cc_start: 0.7083 (ttt90) cc_final: 0.6843 (mtp180) outliers start: 25 outliers final: 10 residues processed: 104 average time/residue: 0.2389 time to fit residues: 35.8609 Evaluate side-chains 95 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 475 PHE 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 146 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 475 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 70 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.191727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.139022 restraints weight = 14359.043| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.72 r_work: 0.3668 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2654 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= 0.181 Angle : 0.554 6.452 13354 Z= 0.308 Chirality : 0.039 0.166 1522 Planarity : 0.003 0.033 1380 Dihedral : 24.336 76.240 1972 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.69 % Allowed : 22.83 % 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: -0.98 (0.26), residues: 920 helix: 0.12 (0.23), residues: 444 sheet: 0.21 (0.62), residues: 64 loop : -1.65 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 41 HIS 0.002 0.001 HIS D 413 PHE 0.014 0.002 PHE A 345 TYR 0.006 0.001 TYR A 488 ARG 0.007 0.001 ARG A 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 113 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8290 (ptpt) cc_final: 0.8015 (mttm) REVERT: A 280 MET cc_start: 0.7712 (ttp) cc_final: 0.6830 (tpt) REVERT: A 357 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6474 (mm) REVERT: A 364 ARG cc_start: 0.7437 (mtt90) cc_final: 0.7105 (ptp-110) REVERT: A 402 TYR cc_start: 0.6365 (m-80) cc_final: 0.5689 (p90) REVERT: D 226 LYS cc_start: 0.8274 (ptpt) cc_final: 0.8031 (mttm) REVERT: D 280 MET cc_start: 0.7025 (ttp) cc_final: 0.6123 (tpt) REVERT: D 392 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7202 (mt-10) REVERT: D 402 TYR cc_start: 0.6277 (m-80) cc_final: 0.5539 (p90) outliers start: 14 outliers final: 6 residues processed: 112 average time/residue: 0.1914 time to fit residues: 31.2307 Evaluate side-chains 102 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 D 336 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.188114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.132509 restraints weight = 14426.206| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.93 r_work: 0.3665 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9614 Z= 0.181 Angle : 0.542 5.902 13354 Z= 0.301 Chirality : 0.038 0.163 1522 Planarity : 0.003 0.031 1380 Dihedral : 24.183 77.745 1972 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.81 % Allowed : 22.71 % 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: -0.88 (0.27), residues: 920 helix: 0.27 (0.23), residues: 444 sheet: 0.15 (0.65), residues: 66 loop : -1.67 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 122 HIS 0.002 0.001 HIS A 413 PHE 0.016 0.001 PHE A 345 TYR 0.018 0.001 TYR D 488 ARG 0.005 0.000 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 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8271 (ptpt) cc_final: 0.8011 (mttm) REVERT: A 280 MET cc_start: 0.7493 (ttp) cc_final: 0.6866 (tpt) REVERT: A 357 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6368 (mm) REVERT: A 402 TYR cc_start: 0.6410 (m-80) cc_final: 0.5744 (p90) REVERT: D 226 LYS cc_start: 0.8329 (ptpt) cc_final: 0.8069 (mttm) REVERT: D 284 LEU cc_start: 0.7428 (mt) cc_final: 0.7181 (mt) REVERT: D 357 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6625 (mm) REVERT: D 392 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7200 (mt-10) outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 0.2746 time to fit residues: 43.2926 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 357 LEU Chi-restraints excluded: chain A residue 430 SER 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 369 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.0470 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.191482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.136379 restraints weight = 14922.376| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.92 r_work: 0.3636 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9614 Z= 0.235 Angle : 0.559 5.977 13354 Z= 0.309 Chirality : 0.039 0.160 1522 Planarity : 0.004 0.041 1380 Dihedral : 24.148 78.190 1972 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.93 % Allowed : 23.07 % Favored : 75.00 % 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: -0.97 (0.26), residues: 920 helix: 0.32 (0.23), residues: 446 sheet: -0.32 (0.72), residues: 48 loop : -1.74 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 400 HIS 0.002 0.001 HIS A 413 PHE 0.012 0.001 PHE A 489 TYR 0.027 0.001 TYR D 73 ARG 0.008 0.000 ARG A 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 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8296 (ptpt) cc_final: 0.8029 (mttm) REVERT: A 280 MET cc_start: 0.7530 (ttp) cc_final: 0.6985 (tpt) REVERT: A 354 ILE cc_start: 0.5251 (OUTLIER) cc_final: 0.5041 (pt) REVERT: A 357 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6386 (mm) REVERT: A 402 TYR cc_start: 0.6422 (m-80) cc_final: 0.5739 (p90) REVERT: D 226 LYS cc_start: 0.8336 (ptpt) cc_final: 0.8080 (mttm) REVERT: D 280 MET cc_start: 0.6914 (ttp) cc_final: 0.6264 (tpt) REVERT: D 354 ILE cc_start: 0.5182 (OUTLIER) cc_final: 0.4979 (pt) REVERT: D 357 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6632 (mm) REVERT: D 392 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7256 (mt-10) REVERT: D 402 TYR cc_start: 0.6305 (m-80) cc_final: 0.5586 (p90) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.1977 time to fit residues: 29.0353 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 354 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 430 SER 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 354 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.5980 chunk 56 optimal weight: 0.0470 chunk 99 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 = 0.4551 r_free = 0.4551 target = 0.196198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.143666 restraints weight = 14470.938| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.79 r_work: 0.3736 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3337 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= 0.159 Angle : 0.534 6.030 13354 Z= 0.295 Chirality : 0.037 0.158 1522 Planarity : 0.003 0.029 1380 Dihedral : 23.872 81.326 1972 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.57 % Allowed : 23.67 % Favored : 74.76 % 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: -0.89 (0.26), residues: 920 helix: 0.30 (0.23), residues: 462 sheet: 0.23 (0.74), residues: 48 loop : -1.74 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 122 HIS 0.003 0.001 HIS A 413 PHE 0.016 0.001 PHE D 489 TYR 0.013 0.001 TYR D 488 ARG 0.006 0.001 ARG A 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 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ILE cc_start: 0.2643 (OUTLIER) cc_final: 0.2193 (pt) REVERT: A 280 MET cc_start: 0.7448 (ttp) cc_final: 0.6958 (tpt) REVERT: A 357 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6367 (mm) REVERT: D 280 MET cc_start: 0.7061 (ttp) cc_final: 0.6342 (tpt) REVERT: D 357 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6496 (mm) REVERT: D 392 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7382 (mt-10) outliers start: 13 outliers final: 4 residues processed: 102 average time/residue: 0.2337 time to fit residues: 33.7587 Evaluate side-chains 93 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 261 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.0170 chunk 19 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.191002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.135283 restraints weight = 14701.786| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.01 r_work: 0.3697 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3482 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= 0.171 Angle : 0.532 5.714 13354 Z= 0.294 Chirality : 0.037 0.159 1522 Planarity : 0.003 0.029 1380 Dihedral : 23.881 79.706 1970 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.45 % Allowed : 24.03 % 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: -0.64 (0.27), residues: 920 helix: 0.56 (0.23), residues: 460 sheet: 0.38 (0.77), residues: 48 loop : -1.69 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 164 HIS 0.002 0.001 HIS A 413 PHE 0.011 0.001 PHE A 489 TYR 0.019 0.001 TYR A 73 ARG 0.006 0.001 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 98 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 261 ILE cc_start: 0.2564 (OUTLIER) cc_final: 0.2085 (pt) REVERT: A 280 MET cc_start: 0.7443 (ttp) cc_final: 0.6940 (tpt) REVERT: A 357 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6335 (mm) REVERT: A 485 ARG cc_start: 0.7136 (ttt90) cc_final: 0.6922 (mmt180) REVERT: D 261 ILE cc_start: 0.3274 (OUTLIER) cc_final: 0.2881 (pt) REVERT: D 280 MET cc_start: 0.7016 (ttp) cc_final: 0.6310 (tpt) REVERT: D 357 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6489 (mm) REVERT: D 392 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7398 (mt-10) REVERT: D 451 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7983 (mmtm) outliers start: 12 outliers final: 4 residues processed: 94 average time/residue: 0.2263 time to fit residues: 29.7788 Evaluate side-chains 91 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 261 ILE 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 451 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 0.0040 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 overall best weight: 0.4410 ------------------------------------------------------------------------------- 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 = 0.4480 r_free = 0.4480 target = 0.192324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.136856 restraints weight = 14487.332| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.97 r_work: 0.3719 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9614 Z= 0.166 Angle : 0.532 5.928 13354 Z= 0.296 Chirality : 0.037 0.168 1522 Planarity : 0.003 0.036 1380 Dihedral : 23.799 80.021 1970 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.33 % Allowed : 23.91 % Favored : 74.76 % 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: -0.55 (0.27), residues: 920 helix: 0.65 (0.23), residues: 460 sheet: 0.42 (0.76), residues: 48 loop : -1.67 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.002 0.000 HIS A 413 PHE 0.012 0.001 PHE A 489 TYR 0.012 0.001 TYR D 73 ARG 0.005 0.000 ARG A 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4790.14 seconds wall clock time: 85 minutes 40.59 seconds (5140.59 seconds total)