Starting phenix.real_space_refine on Sun Jul 27 10:27:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqr_20452/07_2025/6pqr_20452.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqr_20452/07_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_20452/07_2025/6pqr_20452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqr_20452/07_2025/6pqr_20452.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqr_20452/07_2025/6pqr_20452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqr_20452/07_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-5711/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: 6.02, per 1000 atoms: 0.65 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: 5.27 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 240 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 413 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 408 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 243 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 240 " Number of angles added : 4 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 51.7% alpha, 15.8% beta 34 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 3.37 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: 3.00 Time building geometry restraints manager: 2.96 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: 1.320 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.480 Find NCS groups from input model: 0.150 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- 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 9622 Z= 0.410 Angle : 0.857 13.236 13358 Z= 0.506 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 Details of bonding type rmsd hydrogen bonds : bond 0.14442 ( 420) hydrogen bonds : angle 6.83112 ( 1198) metal coordination : bond 0.03271 ( 8) metal coordination : angle 10.25246 ( 4) covalent geometry : bond 0.00903 ( 9614) covalent geometry : angle 0.83906 (13354) *********************** 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 : 0.984 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: 0.2403 time to fit residues: 37.9103 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 : 0.945 ------------------------------------------------------------------------------- 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 9622 Z= 0.155 Angle : 0.616 8.064 13358 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 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 420) hydrogen bonds : angle 4.51751 ( 1198) metal coordination : bond 0.00562 ( 8) metal coordination : angle 2.13079 ( 4) covalent geometry : bond 0.00343 ( 9614) covalent geometry : angle 0.61485 (13354) *********************** 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 : 0.875 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: 0.2088 time to fit residues: 34.2864 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 : 0.928 ------------------------------------------------------------------------------- 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: 6.9990 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.184718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129178 restraints weight = 14328.639| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.92 r_work: 0.3614 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9622 Z= 0.161 Angle : 0.589 9.132 13358 Z= 0.323 Chirality : 0.041 0.236 1522 Planarity : 0.004 0.033 1380 Dihedral : 24.706 68.308 1972 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.93 % Allowed : 18.00 % Favored : 80.07 % 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: -1.48 (0.26), residues: 920 helix: -0.37 (0.22), residues: 444 sheet: -0.02 (0.63), residues: 60 loop : -1.78 (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 0.011 0.002 PHE A 268 TYR 0.008 0.001 TYR A 488 ARG 0.003 0.001 ARG D 343 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 420) hydrogen bonds : angle 4.14808 ( 1198) metal coordination : bond 0.00912 ( 8) metal coordination : angle 2.69370 ( 4) covalent geometry : bond 0.00366 ( 9614) covalent geometry : angle 0.58725 (13354) *********************** 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 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7780 (ttp) cc_final: 0.7215 (ttp) REVERT: A 285 HIS cc_start: 0.7955 (m90) cc_final: 0.7697 (m170) REVERT: A 403 MET cc_start: 0.6419 (mtm) cc_final: 0.6196 (mtp) REVERT: D 220 MET cc_start: 0.8800 (ttp) cc_final: 0.8588 (ttp) REVERT: D 285 HIS cc_start: 0.7915 (m90) cc_final: 0.7666 (m170) outliers start: 16 outliers final: 7 residues processed: 112 average time/residue: 0.2117 time to fit residues: 34.7948 Evaluate side-chains 99 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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: 0.4980 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 D 483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.187070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.131677 restraints weight = 14277.303| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.93 r_work: 0.3650 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9622 Z= 0.134 Angle : 0.559 7.875 13358 Z= 0.310 Chirality : 0.040 0.210 1522 Planarity : 0.003 0.031 1380 Dihedral : 24.530 66.558 1972 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.69 % Allowed : 20.41 % Favored : 77.90 % 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: -1.18 (0.26), residues: 920 helix: -0.11 (0.23), residues: 446 sheet: 0.35 (0.66), residues: 60 loop : -1.69 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 400 HIS 0.002 0.001 HIS D 413 PHE 0.011 0.001 PHE D 292 TYR 0.009 0.001 TYR D 73 ARG 0.004 0.000 ARG D 364 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 420) hydrogen bonds : angle 4.05548 ( 1198) metal coordination : bond 0.00506 ( 8) metal coordination : angle 2.10430 ( 4) covalent geometry : bond 0.00301 ( 9614) covalent geometry : angle 0.55826 (13354) *********************** 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 114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: A 280 MET cc_start: 0.7748 (ttp) cc_final: 0.7416 (ttp) REVERT: A 281 GLU cc_start: 0.7756 (pp20) cc_final: 0.7544 (tm-30) REVERT: A 344 PHE cc_start: 0.8141 (t80) cc_final: 0.7679 (t80) REVERT: A 442 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8348 (mtm-85) REVERT: D 220 MET cc_start: 0.8775 (ttp) cc_final: 0.8567 (ttp) REVERT: D 226 LYS cc_start: 0.8278 (ptpt) cc_final: 0.7995 (mttm) outliers start: 14 outliers final: 7 residues processed: 108 average time/residue: 0.2239 time to fit residues: 33.9908 Evaluate side-chains 106 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.189357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.136499 restraints weight = 14341.514| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.71 r_work: 0.3628 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9622 Z= 0.186 Angle : 0.578 7.984 13358 Z= 0.320 Chirality : 0.041 0.183 1522 Planarity : 0.003 0.032 1380 Dihedral : 24.507 67.903 1972 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.78 % Allowed : 21.26 % Favored : 75.97 % 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: 0.03 (0.23), residues: 448 sheet: 0.25 (0.65), residues: 60 loop : -1.76 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 164 HIS 0.002 0.001 HIS A 447 PHE 0.026 0.002 PHE D 345 TYR 0.013 0.001 TYR D 73 ARG 0.005 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 420) hydrogen bonds : angle 3.98263 ( 1198) metal coordination : bond 0.00699 ( 8) metal coordination : angle 1.03057 ( 4) covalent geometry : bond 0.00433 ( 9614) covalent geometry : angle 0.57799 (13354) *********************** 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 118 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: A 226 LYS cc_start: 0.8289 (ptpt) cc_final: 0.8032 (mttm) REVERT: A 280 MET cc_start: 0.7791 (ttp) cc_final: 0.7486 (ttp) REVERT: A 281 GLU cc_start: 0.7707 (pp20) cc_final: 0.7503 (tm-30) REVERT: A 402 TYR cc_start: 0.6191 (m-80) cc_final: 0.5436 (p90) REVERT: D 220 MET cc_start: 0.8808 (ttp) cc_final: 0.8592 (ttp) REVERT: D 226 LYS cc_start: 0.8309 (ptpt) cc_final: 0.8041 (mttm) REVERT: D 280 MET cc_start: 0.7270 (ttp) cc_final: 0.7017 (ttp) REVERT: D 402 TYR cc_start: 0.6173 (m-80) cc_final: 0.5433 (p90) outliers start: 23 outliers final: 7 residues processed: 109 average time/residue: 0.2215 time to fit residues: 34.8658 Evaluate side-chains 99 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 146 ILE 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 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.191059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.135617 restraints weight = 14826.786| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.93 r_work: 0.3632 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9622 Z= 0.161 Angle : 0.559 6.228 13358 Z= 0.309 Chirality : 0.040 0.166 1522 Planarity : 0.004 0.040 1380 Dihedral : 24.344 73.670 1972 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.17 % Allowed : 21.62 % 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: -0.98 (0.26), residues: 920 helix: 0.15 (0.23), residues: 448 sheet: 0.30 (0.64), residues: 64 loop : -1.70 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 41 HIS 0.002 0.001 HIS A 413 PHE 0.018 0.002 PHE D 345 TYR 0.006 0.001 TYR A 62 ARG 0.008 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 420) hydrogen bonds : angle 3.89251 ( 1198) metal coordination : bond 0.00298 ( 8) metal coordination : angle 1.34499 ( 4) covalent geometry : bond 0.00370 ( 9614) covalent geometry : angle 0.55853 (13354) *********************** 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: 18 poor density : 95 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8285 (ptpt) cc_final: 0.8042 (mttm) REVERT: A 280 MET cc_start: 0.7555 (ttp) cc_final: 0.6804 (tpt) REVERT: A 357 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6374 (mm) REVERT: A 402 TYR cc_start: 0.6084 (m-80) cc_final: 0.5341 (p90) REVERT: D 220 MET cc_start: 0.8831 (ttp) cc_final: 0.8620 (ttp) REVERT: D 226 LYS cc_start: 0.8314 (ptpt) cc_final: 0.8057 (mttm) REVERT: D 280 MET cc_start: 0.7145 (ttp) cc_final: 0.6211 (tpt) REVERT: D 357 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6555 (mm) REVERT: D 402 TYR cc_start: 0.6062 (m-80) cc_final: 0.5346 (p90) outliers start: 18 outliers final: 10 residues processed: 110 average time/residue: 0.2105 time to fit residues: 33.3304 Evaluate side-chains 103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 430 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN D 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.192420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.139603 restraints weight = 14445.646| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.75 r_work: 0.3683 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9622 Z= 0.130 Angle : 0.538 5.789 13358 Z= 0.299 Chirality : 0.038 0.160 1522 Planarity : 0.003 0.031 1380 Dihedral : 24.131 77.331 1972 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.17 % Allowed : 21.86 % Favored : 75.97 % 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: -0.99 (0.26), residues: 920 helix: 0.28 (0.23), residues: 448 sheet: -0.30 (0.71), residues: 48 loop : -1.75 (0.29), residues: 424 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 0.012 0.001 PHE A 489 TYR 0.019 0.001 TYR A 488 ARG 0.006 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 420) hydrogen bonds : angle 3.79422 ( 1198) metal coordination : bond 0.00314 ( 8) metal coordination : angle 1.43752 ( 4) covalent geometry : bond 0.00291 ( 9614) covalent geometry : angle 0.53761 (13354) *********************** 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 119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8315 (ptpt) cc_final: 0.8085 (mttm) REVERT: A 280 MET cc_start: 0.7530 (ttp) cc_final: 0.6953 (tpt) REVERT: A 357 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6438 (mm) REVERT: A 402 TYR cc_start: 0.6230 (m-80) cc_final: 0.5548 (p90) REVERT: A 442 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.8220 (mtm-85) REVERT: D 220 MET cc_start: 0.8778 (ttp) cc_final: 0.8577 (ttp) REVERT: D 226 LYS cc_start: 0.8310 (ptpt) cc_final: 0.8051 (mttm) REVERT: D 354 ILE cc_start: 0.5311 (OUTLIER) cc_final: 0.5103 (pt) REVERT: D 357 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6607 (mm) REVERT: D 402 TYR cc_start: 0.6094 (m-80) cc_final: 0.5379 (p90) REVERT: D 451 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8042 (mmtm) outliers start: 18 outliers final: 9 residues processed: 113 average time/residue: 0.1994 time to fit residues: 32.8164 Evaluate side-chains 106 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 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 367 VAL Chi-restraints excluded: chain D residue 451 LYS 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: 0.4980 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.181239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.124603 restraints weight = 14628.722| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.95 r_work: 0.3548 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 9622 Z= 0.308 Angle : 0.676 6.007 13358 Z= 0.367 Chirality : 0.045 0.181 1522 Planarity : 0.004 0.044 1380 Dihedral : 24.382 77.109 1972 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.02 % Allowed : 21.62 % Favored : 75.36 % 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: -1.29 (0.26), residues: 920 helix: 0.01 (0.23), residues: 452 sheet: -0.74 (0.71), residues: 46 loop : -1.84 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 400 HIS 0.004 0.001 HIS A 408 PHE 0.017 0.002 PHE A 345 TYR 0.045 0.002 TYR A 73 ARG 0.010 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 420) hydrogen bonds : angle 4.06359 ( 1198) metal coordination : bond 0.01543 ( 8) metal coordination : angle 0.73314 ( 4) covalent geometry : bond 0.00720 ( 9614) covalent geometry : angle 0.67559 (13354) *********************** 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 109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8330 (ptpt) cc_final: 0.8070 (mttm) REVERT: A 280 MET cc_start: 0.7615 (ttp) cc_final: 0.7031 (tpt) REVERT: A 357 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6553 (mm) REVERT: A 392 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 402 TYR cc_start: 0.6167 (m-80) cc_final: 0.5582 (p90) REVERT: D 220 MET cc_start: 0.8893 (ttp) cc_final: 0.8674 (ttp) REVERT: D 226 LYS cc_start: 0.8339 (ptpt) cc_final: 0.8079 (mttm) REVERT: D 280 MET cc_start: 0.7062 (ttp) cc_final: 0.6146 (tpt) REVERT: D 357 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6543 (mm) REVERT: D 402 TYR cc_start: 0.6115 (m-80) cc_final: 0.5501 (p90) outliers start: 25 outliers final: 15 residues processed: 101 average time/residue: 0.2812 time to fit residues: 40.1576 Evaluate side-chains 99 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 475 PHE 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 272 THR Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 475 PHE 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: 0.9990 chunk 99 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.187132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.131608 restraints weight = 14441.430| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.92 r_work: 0.3648 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9622 Z= 0.134 Angle : 0.558 5.977 13358 Z= 0.309 Chirality : 0.039 0.158 1522 Planarity : 0.003 0.033 1380 Dihedral : 24.067 84.300 1972 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -1.02 (0.27), residues: 920 helix: 0.29 (0.23), residues: 448 sheet: -0.38 (0.72), residues: 48 loop : -1.80 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 122 HIS 0.003 0.001 HIS A 413 PHE 0.012 0.001 PHE A 489 TYR 0.027 0.001 TYR A 73 ARG 0.009 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 420) hydrogen bonds : angle 3.79568 ( 1198) metal coordination : bond 0.00524 ( 8) metal coordination : angle 1.12303 ( 4) covalent geometry : bond 0.00303 ( 9614) covalent geometry : angle 0.55747 (13354) *********************** 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 103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8274 (ptpt) cc_final: 0.8050 (mttm) REVERT: A 280 MET cc_start: 0.7533 (ttp) cc_final: 0.6982 (tpt) REVERT: A 354 ILE cc_start: 0.5198 (OUTLIER) cc_final: 0.4968 (pt) REVERT: A 357 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6517 (mm) REVERT: A 364 ARG cc_start: 0.7405 (mtt90) cc_final: 0.7097 (ptp-110) REVERT: A 392 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7192 (mt-10) REVERT: A 402 TYR cc_start: 0.6463 (m-80) cc_final: 0.5705 (p90) REVERT: A 403 MET cc_start: 0.6361 (tpp) cc_final: 0.5891 (tpp) REVERT: D 185 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8033 (tm-30) REVERT: D 226 LYS cc_start: 0.8298 (ptpt) cc_final: 0.8038 (mttm) REVERT: D 280 MET cc_start: 0.7047 (ttp) cc_final: 0.6212 (tpt) REVERT: D 354 ILE cc_start: 0.5165 (OUTLIER) cc_final: 0.4952 (pt) REVERT: D 357 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6554 (mm) REVERT: D 402 TYR cc_start: 0.6166 (m-80) cc_final: 0.5475 (p90) outliers start: 11 outliers final: 5 residues processed: 101 average time/residue: 0.1973 time to fit residues: 28.7649 Evaluate side-chains 99 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 354 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 354 ILE 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: 0.6980 chunk 13 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 19 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.188666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.133271 restraints weight = 14651.170| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.93 r_work: 0.3668 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9622 Z= 0.131 Angle : 0.542 5.993 13358 Z= 0.300 Chirality : 0.038 0.157 1522 Planarity : 0.003 0.031 1380 Dihedral : 23.960 84.124 1972 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.21 % Allowed : 23.79 % 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: -0.95 (0.27), residues: 920 helix: 0.31 (0.23), residues: 460 sheet: -0.17 (0.74), residues: 48 loop : -1.78 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 164 HIS 0.003 0.001 HIS A 413 PHE 0.013 0.001 PHE A 489 TYR 0.027 0.001 TYR A 73 ARG 0.004 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 420) hydrogen bonds : angle 3.72523 ( 1198) metal coordination : bond 0.00316 ( 8) metal coordination : angle 0.88758 ( 4) covalent geometry : bond 0.00298 ( 9614) covalent geometry : angle 0.54181 (13354) ********************** 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 100 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 261 ILE cc_start: 0.2322 (OUTLIER) cc_final: 0.1876 (pt) REVERT: A 280 MET cc_start: 0.7504 (ttp) cc_final: 0.6969 (tpt) REVERT: A 357 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6389 (mm) REVERT: A 364 ARG cc_start: 0.7413 (mtt90) cc_final: 0.7167 (ptm160) REVERT: A 392 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7182 (mt-10) REVERT: A 402 TYR cc_start: 0.6490 (m-80) cc_final: 0.5683 (p90) REVERT: A 403 MET cc_start: 0.6395 (tpp) cc_final: 0.5965 (tpp) REVERT: A 442 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8008 (mtt-85) REVERT: D 185 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8061 (tm-30) REVERT: D 226 LYS cc_start: 0.8320 (ptpt) cc_final: 0.8085 (mttm) REVERT: D 280 MET cc_start: 0.6947 (ttp) cc_final: 0.6152 (tpt) REVERT: D 357 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6595 (mm) REVERT: D 402 TYR cc_start: 0.6307 (m-80) cc_final: 0.5616 (p90) outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 0.2215 time to fit residues: 31.1418 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 : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 79 VAL 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 17 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.0170 chunk 41 optimal weight: 0.0370 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 14 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 overall best weight: 0.4074 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.195675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.141429 restraints weight = 14843.689| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.93 r_work: 0.3709 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9622 Z= 0.119 Angle : 0.528 5.950 13358 Z= 0.293 Chirality : 0.037 0.155 1522 Planarity : 0.003 0.029 1380 Dihedral : 23.832 84.881 1972 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.09 % Allowed : 24.03 % 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: -0.73 (0.27), residues: 920 helix: 0.48 (0.23), residues: 462 sheet: 0.06 (0.75), residues: 48 loop : -1.70 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 164 HIS 0.003 0.000 HIS A 413 PHE 0.016 0.001 PHE A 317 TYR 0.025 0.001 TYR A 73 ARG 0.004 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 420) hydrogen bonds : angle 3.69042 ( 1198) metal coordination : bond 0.00188 ( 8) metal coordination : angle 0.98842 ( 4) covalent geometry : bond 0.00263 ( 9614) covalent geometry : angle 0.52769 (13354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4904.72 seconds wall clock time: 87 minutes 7.24 seconds (5227.24 seconds total)