Starting phenix.real_space_refine on Fri Aug 22 19:22:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9g_40240/08_2025/8s9g_40240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9g_40240/08_2025/8s9g_40240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s9g_40240/08_2025/8s9g_40240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9g_40240/08_2025/8s9g_40240.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9g_40240/08_2025/8s9g_40240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9g_40240/08_2025/8s9g_40240.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.133 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4529 2.51 5 N 1221 2.21 5 O 1214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7004 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4027 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 219} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 549} Chain breaks: 1 Unresolved non-hydrogen bonds: 665 Unresolved non-hydrogen angles: 847 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLU:plan': 32, 'ASP:plan': 24, 'GLN:plan1': 16, 'ARG:plan': 3, 'ASN:plan1': 14, 'TYR:plan': 2, 'HIS:plan': 5, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 375 Chain: "E" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1314 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 2 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASN:plan1': 8, 'ARG:plan': 2, 'ASP:plan': 6, 'TYR:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "H" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 837 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "L" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 696 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.70, per 1000 atoms: 0.24 Number of scatterers: 7004 At special positions: 0 Unit cell: (81, 98, 119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1214 8.00 N 1221 7.00 C 4529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.07 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.16 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.06 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.07 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 Links applied ALPHA1-6 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " BETA1-6 " NAG B 1 " - " FUC B 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 90 " " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 103 " " NAG B 1 " - " ASN E 343 " " NAG E 601 " - " ASN E 354 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 264.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 46.9% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 Processing helix chain 'A' and resid 55 through 77 Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.314A pdb=" N GLN A 81 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.546A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.930A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 4.337A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.743A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.297A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.519A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.860A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.650A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.747A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.896A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 597 removed outlier: 3.797A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 366 through 370 Processing helix chain 'E' and resid 386 through 390 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.511A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.518A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.529A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.977A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 33 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.976A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.185A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.819A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.819A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.586A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.549A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.994A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.593A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA L 35 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.593A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA L 35 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1570 1.33 - 1.45: 1801 1.45 - 1.58: 3762 1.58 - 1.70: 4 1.70 - 1.83: 62 Bond restraints: 7199 Sorted by residual: bond pdb=" N PRO A 178 " pdb=" CD PRO A 178 " ideal model delta sigma weight residual 1.473 1.596 -0.123 1.40e-02 5.10e+03 7.76e+01 bond pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 1.525 1.584 -0.059 1.27e-02 6.20e+03 2.13e+01 bond pdb=" N ARG A 514 " pdb=" CA ARG A 514 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.35e-02 5.49e+03 8.17e+00 bond pdb=" CG PHE E 374 " pdb=" CD1 PHE E 374 " ideal model delta sigma weight residual 1.384 1.443 -0.059 2.10e-02 2.27e+03 7.81e+00 bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.586 -0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 7194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 9567 3.05 - 6.09: 239 6.09 - 9.14: 54 9.14 - 12.19: 0 12.19 - 15.24: 1 Bond angle restraints: 9861 Sorted by residual: angle pdb=" N LYS E 378 " pdb=" CA LYS E 378 " pdb=" C LYS E 378 " ideal model delta sigma weight residual 107.99 123.23 -15.24 1.77e+00 3.19e-01 7.41e+01 angle pdb=" C GLY A 537 " pdb=" N PRO A 538 " pdb=" CA PRO A 538 " ideal model delta sigma weight residual 119.76 127.62 -7.86 1.03e+00 9.43e-01 5.82e+01 angle pdb=" C ARG E 498 " pdb=" N PRO E 499 " pdb=" CA PRO E 499 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.02e+00 9.61e-01 5.60e+01 angle pdb=" C GLU A 489 " pdb=" N PRO A 490 " pdb=" CA PRO A 490 " ideal model delta sigma weight residual 119.56 126.93 -7.37 1.01e+00 9.80e-01 5.32e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.78 127.18 -7.40 1.03e+00 9.43e-01 5.17e+01 ... (remaining 9856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 4107 21.51 - 43.02: 105 43.02 - 64.53: 21 64.53 - 86.05: 9 86.05 - 107.56: 4 Dihedral angle restraints: 4246 sinusoidal: 1386 harmonic: 2860 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 60.37 32.63 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.85 107.56 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.15 106.77 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 4243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 912 0.097 - 0.194: 151 0.194 - 0.290: 28 0.290 - 0.387: 4 0.387 - 0.484: 1 Chirality restraints: 1096 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.68e+01 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.30e+01 chirality pdb=" C1 FUC B 5 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 5 " pdb=" O5 FUC B 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.57e+00 ... (remaining 1093 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 53 " -0.082 2.00e-02 2.50e+03 1.36e-01 2.32e+02 pdb=" CG ASN A 53 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 53 " -0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN A 53 " 0.241 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 90 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C GLN L 90 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN L 90 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN L 91 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 41 " 0.025 2.00e-02 2.50e+03 1.28e-02 3.29e+00 pdb=" CG TYR A 41 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 41 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 41 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 41 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 41 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 41 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 41 " 0.014 2.00e-02 2.50e+03 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 35 2.63 - 3.20: 6053 3.20 - 3.77: 10622 3.77 - 4.33: 15098 4.33 - 4.90: 24255 Nonbonded interactions: 56063 Sorted by model distance: nonbonded pdb=" OE2 GLU A 208 " pdb=" ND2 ASN A 210 " model vdw 2.064 3.120 nonbonded pdb=" O ASN E 417 " pdb=" ND2 ASN E 417 " model vdw 2.175 3.120 nonbonded pdb=" O VAL A 212 " pdb=" OD1 ASP A 216 " model vdw 2.236 3.040 nonbonded pdb=" NH2 ARG A 177 " pdb=" O LYS A 470 " model vdw 2.331 3.120 nonbonded pdb=" O LYS A 465 " pdb=" N GLU A 467 " model vdw 2.406 3.120 ... (remaining 56058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 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 : 0.010 0.129 7218 Z= 0.570 Angle : 1.347 30.737 9909 Z= 0.908 Chirality : 0.079 0.484 1096 Planarity : 0.005 0.023 1280 Dihedral : 11.614 107.558 2389 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.16 % Favored : 97.63 % Rotamer: Outliers : 1.22 % Allowed : 1.43 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.26), residues: 972 helix: -0.47 (0.24), residues: 387 sheet: 0.17 (0.39), residues: 153 loop : 0.30 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 192 TYR 0.025 0.004 TYR A 41 PHE 0.019 0.003 PHE A 32 TRP 0.017 0.004 TRP H 117 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00979 ( 7199) covalent geometry : angle 1.29210 ( 9861) SS BOND : bond 0.04792 ( 9) SS BOND : angle 3.61559 ( 18) hydrogen bonds : bond 0.21910 ( 363) hydrogen bonds : angle 7.08183 ( 993) link_ALPHA1-6 : bond 0.05456 ( 1) link_ALPHA1-6 : angle 1.62842 ( 3) link_BETA1-4 : bond 0.05840 ( 2) link_BETA1-4 : angle 3.35659 ( 6) link_BETA1-6 : bond 0.04779 ( 1) link_BETA1-6 : angle 2.25770 ( 3) link_NAG-ASN : bond 0.05256 ( 6) link_NAG-ASN : angle 8.14650 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 453 TYR cc_start: 0.7135 (p90) cc_final: 0.6898 (p90) REVERT: L 55 ARG cc_start: 0.6629 (ttm110) cc_final: 0.6366 (ttp80) outliers start: 6 outliers final: 1 residues processed: 98 average time/residue: 0.3680 time to fit residues: 38.4310 Evaluate side-chains 62 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 354 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0170 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 417 HIS E 474 GLN L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.217331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.194879 restraints weight = 6815.623| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.49 r_work: 0.3991 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7218 Z= 0.140 Angle : 0.629 13.945 9909 Z= 0.319 Chirality : 0.043 0.209 1096 Planarity : 0.004 0.046 1280 Dihedral : 7.247 70.141 1264 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.83 % Allowed : 7.94 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.27), residues: 972 helix: 0.85 (0.26), residues: 382 sheet: 0.41 (0.40), residues: 152 loop : 0.45 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 559 TYR 0.018 0.002 TYR A 516 PHE 0.017 0.002 PHE A 314 TRP 0.011 0.001 TRP H 117 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7199) covalent geometry : angle 0.58033 ( 9861) SS BOND : bond 0.00860 ( 9) SS BOND : angle 1.44247 ( 18) hydrogen bonds : bond 0.05669 ( 363) hydrogen bonds : angle 5.17339 ( 993) link_ALPHA1-6 : bond 0.00657 ( 1) link_ALPHA1-6 : angle 1.78594 ( 3) link_BETA1-4 : bond 0.00587 ( 2) link_BETA1-4 : angle 2.92138 ( 6) link_BETA1-6 : bond 0.00617 ( 1) link_BETA1-6 : angle 1.23226 ( 3) link_NAG-ASN : bond 0.00513 ( 6) link_NAG-ASN : angle 5.25171 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 53 ASN cc_start: 0.4025 (OUTLIER) cc_final: 0.3651 (m-40) REVERT: A 61 ASN cc_start: 0.7098 (m-40) cc_final: 0.6893 (m-40) REVERT: A 97 LEU cc_start: 0.7220 (tp) cc_final: 0.6700 (tp) REVERT: A 247 LYS cc_start: 0.6080 (mmtt) cc_final: 0.5725 (pptt) REVERT: A 249 MET cc_start: 0.5955 (mtp) cc_final: 0.5609 (mpm) REVERT: H 90 ASP cc_start: 0.5788 (m-30) cc_final: 0.5516 (m-30) REVERT: L 55 ARG cc_start: 0.7314 (ttm110) cc_final: 0.6867 (mtm110) outliers start: 9 outliers final: 3 residues processed: 77 average time/residue: 0.4850 time to fit residues: 39.8674 Evaluate side-chains 67 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 472 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 210 ASN E 474 GLN E 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.207673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.184034 restraints weight = 6874.750| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.64 r_work: 0.3879 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 7218 Z= 0.213 Angle : 0.683 11.882 9909 Z= 0.346 Chirality : 0.045 0.297 1096 Planarity : 0.005 0.046 1280 Dihedral : 6.190 45.274 1264 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.05 % Allowed : 9.78 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.27), residues: 972 helix: 0.45 (0.26), residues: 383 sheet: 0.41 (0.41), residues: 151 loop : 0.13 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 393 TYR 0.027 0.003 TYR A 385 PHE 0.024 0.003 PHE E 429 TRP 0.015 0.002 TRP A 473 HIS 0.007 0.002 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 7199) covalent geometry : angle 0.64751 ( 9861) SS BOND : bond 0.01045 ( 9) SS BOND : angle 2.70641 ( 18) hydrogen bonds : bond 0.05933 ( 363) hydrogen bonds : angle 5.22567 ( 993) link_ALPHA1-6 : bond 0.00550 ( 1) link_ALPHA1-6 : angle 1.74472 ( 3) link_BETA1-4 : bond 0.00734 ( 2) link_BETA1-4 : angle 2.95398 ( 6) link_BETA1-6 : bond 0.00131 ( 1) link_BETA1-6 : angle 1.26263 ( 3) link_NAG-ASN : bond 0.00479 ( 6) link_NAG-ASN : angle 4.01961 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7285 (tp) cc_final: 0.6811 (tp) REVERT: A 247 LYS cc_start: 0.6165 (mmtt) cc_final: 0.5935 (mttt) REVERT: A 249 MET cc_start: 0.6455 (mtp) cc_final: 0.5939 (mtp) REVERT: H 38 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6457 (ttp-170) REVERT: H 90 ASP cc_start: 0.5847 (m-30) cc_final: 0.5479 (m-30) REVERT: L 55 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7384 (mtt90) outliers start: 15 outliers final: 6 residues processed: 88 average time/residue: 0.4893 time to fit residues: 46.0649 Evaluate side-chains 73 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 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 34 HIS A 397 ASN E 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.208491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184167 restraints weight = 6979.191| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.62 r_work: 0.3890 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7218 Z= 0.142 Angle : 0.598 11.944 9909 Z= 0.300 Chirality : 0.043 0.303 1096 Planarity : 0.004 0.043 1280 Dihedral : 5.477 41.354 1264 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.85 % Allowed : 10.39 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.27), residues: 972 helix: 0.79 (0.26), residues: 375 sheet: 0.52 (0.41), residues: 151 loop : 0.17 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.013 0.002 TYR A 521 PHE 0.012 0.002 PHE L 98 TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7199) covalent geometry : angle 0.56922 ( 9861) SS BOND : bond 0.00858 ( 9) SS BOND : angle 2.20869 ( 18) hydrogen bonds : bond 0.04803 ( 363) hydrogen bonds : angle 4.93177 ( 993) link_ALPHA1-6 : bond 0.00460 ( 1) link_ALPHA1-6 : angle 1.64760 ( 3) link_BETA1-4 : bond 0.00497 ( 2) link_BETA1-4 : angle 2.69573 ( 6) link_BETA1-6 : bond 0.00173 ( 1) link_BETA1-6 : angle 1.36748 ( 3) link_NAG-ASN : bond 0.00390 ( 6) link_NAG-ASN : angle 3.35084 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7289 (tp) cc_final: 0.6770 (tp) REVERT: A 247 LYS cc_start: 0.6170 (mmtt) cc_final: 0.5582 (pptt) REVERT: A 249 MET cc_start: 0.6108 (mtp) cc_final: 0.5835 (mtp) REVERT: H 38 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6478 (ttp-170) REVERT: H 90 ASP cc_start: 0.5855 (m-30) cc_final: 0.5607 (m-30) REVERT: L 55 ARG cc_start: 0.7502 (ttm110) cc_final: 0.7042 (mtm110) outliers start: 14 outliers final: 3 residues processed: 76 average time/residue: 0.4893 time to fit residues: 39.8148 Evaluate side-chains 64 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 38 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN E 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.209282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.185940 restraints weight = 6908.322| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 1.52 r_work: 0.3898 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 7218 Z= 0.139 Angle : 0.560 12.135 9909 Z= 0.285 Chirality : 0.042 0.257 1096 Planarity : 0.004 0.043 1280 Dihedral : 4.862 40.892 1264 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.46 % Allowed : 9.98 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.27), residues: 972 helix: 1.05 (0.27), residues: 369 sheet: 0.64 (0.42), residues: 155 loop : 0.10 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 98 TYR 0.015 0.002 TYR E 453 PHE 0.011 0.002 PHE A 315 TRP 0.020 0.001 TRP H 47 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7199) covalent geometry : angle 0.53975 ( 9861) SS BOND : bond 0.00765 ( 9) SS BOND : angle 2.21888 ( 18) hydrogen bonds : bond 0.04696 ( 363) hydrogen bonds : angle 4.79673 ( 993) link_ALPHA1-6 : bond 0.00553 ( 1) link_ALPHA1-6 : angle 1.52560 ( 3) link_BETA1-4 : bond 0.00514 ( 2) link_BETA1-4 : angle 2.37839 ( 6) link_BETA1-6 : bond 0.00081 ( 1) link_BETA1-6 : angle 1.33671 ( 3) link_NAG-ASN : bond 0.00490 ( 6) link_NAG-ASN : angle 2.36443 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7310 (tp) cc_final: 0.6833 (tp) REVERT: A 247 LYS cc_start: 0.6402 (mmtt) cc_final: 0.5661 (pptt) REVERT: A 249 MET cc_start: 0.6502 (mtp) cc_final: 0.6115 (mtp) REVERT: E 508 TYR cc_start: 0.8150 (m-80) cc_final: 0.7950 (m-80) REVERT: H 38 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6478 (ttp-170) REVERT: H 90 ASP cc_start: 0.5881 (m-30) cc_final: 0.5542 (m-30) REVERT: L 55 ARG cc_start: 0.7678 (ttm110) cc_final: 0.7397 (mtt90) outliers start: 17 outliers final: 7 residues processed: 82 average time/residue: 0.4795 time to fit residues: 42.0929 Evaluate side-chains 70 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain H residue 38 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 0.0970 chunk 61 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.0050 chunk 49 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.212598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189344 restraints weight = 6877.193| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.53 r_work: 0.3931 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 7218 Z= 0.106 Angle : 0.520 10.705 9909 Z= 0.262 Chirality : 0.040 0.233 1096 Planarity : 0.004 0.044 1280 Dihedral : 4.447 39.619 1264 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.24 % Allowed : 11.61 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.27), residues: 972 helix: 1.29 (0.27), residues: 376 sheet: 0.58 (0.41), residues: 158 loop : 0.26 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.018 0.001 TYR E 351 PHE 0.014 0.001 PHE A 315 TRP 0.019 0.001 TRP H 47 HIS 0.004 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 7199) covalent geometry : angle 0.50233 ( 9861) SS BOND : bond 0.00567 ( 9) SS BOND : angle 1.88498 ( 18) hydrogen bonds : bond 0.04050 ( 363) hydrogen bonds : angle 4.58862 ( 993) link_ALPHA1-6 : bond 0.00548 ( 1) link_ALPHA1-6 : angle 1.37968 ( 3) link_BETA1-4 : bond 0.00483 ( 2) link_BETA1-4 : angle 2.07622 ( 6) link_BETA1-6 : bond 0.00193 ( 1) link_BETA1-6 : angle 1.30660 ( 3) link_NAG-ASN : bond 0.00373 ( 6) link_NAG-ASN : angle 2.18872 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7214 (tp) cc_final: 0.6783 (tp) REVERT: A 247 LYS cc_start: 0.6273 (mmtt) cc_final: 0.5649 (pptt) REVERT: A 249 MET cc_start: 0.6493 (mtp) cc_final: 0.6207 (mtp) REVERT: H 38 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6355 (ttp-170) REVERT: H 90 ASP cc_start: 0.5806 (m-30) cc_final: 0.5490 (m-30) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.4856 time to fit residues: 40.0083 Evaluate side-chains 68 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.207686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183491 restraints weight = 6973.128| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 1.58 r_work: 0.3870 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 7218 Z= 0.170 Angle : 0.599 13.554 9909 Z= 0.304 Chirality : 0.042 0.271 1096 Planarity : 0.005 0.057 1280 Dihedral : 4.780 41.425 1264 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.44 % Allowed : 11.61 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.27), residues: 972 helix: 0.83 (0.26), residues: 392 sheet: 0.62 (0.41), residues: 154 loop : 0.01 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 559 TYR 0.018 0.002 TYR A 385 PHE 0.014 0.002 PHE A 274 TRP 0.026 0.002 TRP H 47 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7199) covalent geometry : angle 0.58209 ( 9861) SS BOND : bond 0.00893 ( 9) SS BOND : angle 2.22005 ( 18) hydrogen bonds : bond 0.05050 ( 363) hydrogen bonds : angle 4.82370 ( 993) link_ALPHA1-6 : bond 0.00452 ( 1) link_ALPHA1-6 : angle 1.31364 ( 3) link_BETA1-4 : bond 0.00436 ( 2) link_BETA1-4 : angle 2.09455 ( 6) link_BETA1-6 : bond 0.00062 ( 1) link_BETA1-6 : angle 1.40378 ( 3) link_NAG-ASN : bond 0.00466 ( 6) link_NAG-ASN : angle 2.22314 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7318 (tp) cc_final: 0.6842 (tp) REVERT: H 38 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6357 (ttp-170) REVERT: H 90 ASP cc_start: 0.5920 (m-30) cc_final: 0.5624 (m-30) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.4523 time to fit residues: 35.1002 Evaluate side-chains 69 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain H residue 38 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 43 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.207924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.184414 restraints weight = 6936.209| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.53 r_work: 0.3893 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 7218 Z= 0.142 Angle : 0.562 13.084 9909 Z= 0.287 Chirality : 0.042 0.260 1096 Planarity : 0.004 0.049 1280 Dihedral : 4.650 40.579 1264 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.65 % Allowed : 12.63 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.27), residues: 972 helix: 0.95 (0.26), residues: 390 sheet: 0.55 (0.41), residues: 154 loop : -0.03 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 559 TYR 0.015 0.002 TYR E 351 PHE 0.015 0.002 PHE A 315 TRP 0.028 0.002 TRP H 47 HIS 0.004 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7199) covalent geometry : angle 0.54652 ( 9861) SS BOND : bond 0.00782 ( 9) SS BOND : angle 1.99969 ( 18) hydrogen bonds : bond 0.04605 ( 363) hydrogen bonds : angle 4.73711 ( 993) link_ALPHA1-6 : bond 0.00645 ( 1) link_ALPHA1-6 : angle 1.33412 ( 3) link_BETA1-4 : bond 0.00447 ( 2) link_BETA1-4 : angle 1.94512 ( 6) link_BETA1-6 : bond 0.00081 ( 1) link_BETA1-6 : angle 1.35047 ( 3) link_NAG-ASN : bond 0.00408 ( 6) link_NAG-ASN : angle 2.14531 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7315 (tp) cc_final: 0.6841 (tp) REVERT: A 247 LYS cc_start: 0.5932 (mmmt) cc_final: 0.5428 (pptt) REVERT: H 38 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6488 (ttp-170) REVERT: H 90 ASP cc_start: 0.5985 (m-30) cc_final: 0.5720 (m-30) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.4330 time to fit residues: 34.2397 Evaluate side-chains 70 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 38 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 93 optimal weight: 9.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.209955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.187005 restraints weight = 6935.751| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.48 r_work: 0.3907 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7218 Z= 0.126 Angle : 0.551 12.814 9909 Z= 0.279 Chirality : 0.041 0.250 1096 Planarity : 0.004 0.046 1280 Dihedral : 4.539 39.904 1264 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.44 % Allowed : 13.44 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.27), residues: 972 helix: 1.10 (0.26), residues: 390 sheet: 0.48 (0.41), residues: 156 loop : 0.01 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 559 TYR 0.015 0.001 TYR E 351 PHE 0.020 0.002 PHE H 64 TRP 0.024 0.001 TRP H 47 HIS 0.005 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7199) covalent geometry : angle 0.53737 ( 9861) SS BOND : bond 0.00701 ( 9) SS BOND : angle 1.83508 ( 18) hydrogen bonds : bond 0.04394 ( 363) hydrogen bonds : angle 4.68252 ( 993) link_ALPHA1-6 : bond 0.00628 ( 1) link_ALPHA1-6 : angle 1.35963 ( 3) link_BETA1-4 : bond 0.00449 ( 2) link_BETA1-4 : angle 1.88485 ( 6) link_BETA1-6 : bond 0.00085 ( 1) link_BETA1-6 : angle 1.32267 ( 3) link_NAG-ASN : bond 0.00385 ( 6) link_NAG-ASN : angle 2.00620 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7247 (tp) cc_final: 0.6787 (tp) REVERT: H 38 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6472 (ttp-170) REVERT: H 90 ASP cc_start: 0.6028 (m-30) cc_final: 0.5685 (m-30) REVERT: H 91 THR cc_start: 0.7283 (t) cc_final: 0.6827 (p) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.4351 time to fit residues: 34.2570 Evaluate side-chains 71 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 0.1980 chunk 55 optimal weight: 0.0980 chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.210724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.187757 restraints weight = 6896.819| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 1.49 r_work: 0.3918 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7218 Z= 0.121 Angle : 0.552 12.622 9909 Z= 0.277 Chirality : 0.041 0.244 1096 Planarity : 0.004 0.047 1280 Dihedral : 4.454 39.606 1264 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.44 % Allowed : 13.65 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.28), residues: 972 helix: 1.16 (0.27), residues: 390 sheet: 0.56 (0.41), residues: 155 loop : 0.02 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 559 TYR 0.016 0.001 TYR E 351 PHE 0.021 0.002 PHE H 64 TRP 0.022 0.001 TRP H 47 HIS 0.005 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7199) covalent geometry : angle 0.53900 ( 9861) SS BOND : bond 0.00684 ( 9) SS BOND : angle 1.76933 ( 18) hydrogen bonds : bond 0.04286 ( 363) hydrogen bonds : angle 4.62758 ( 993) link_ALPHA1-6 : bond 0.00629 ( 1) link_ALPHA1-6 : angle 1.36995 ( 3) link_BETA1-4 : bond 0.00439 ( 2) link_BETA1-4 : angle 1.83851 ( 6) link_BETA1-6 : bond 0.00168 ( 1) link_BETA1-6 : angle 1.34036 ( 3) link_NAG-ASN : bond 0.00375 ( 6) link_NAG-ASN : angle 1.99591 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7224 (tp) cc_final: 0.6782 (tp) REVERT: A 247 LYS cc_start: 0.5915 (mmmt) cc_final: 0.5378 (pptt) REVERT: H 38 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6354 (ttp-170) REVERT: H 90 ASP cc_start: 0.5988 (m-30) cc_final: 0.5710 (m-30) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.4296 time to fit residues: 34.8773 Evaluate side-chains 72 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.210237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.187437 restraints weight = 6840.027| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.47 r_work: 0.3919 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7218 Z= 0.125 Angle : 0.546 12.549 9909 Z= 0.277 Chirality : 0.041 0.246 1096 Planarity : 0.004 0.046 1280 Dihedral : 4.443 39.547 1264 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.24 % Allowed : 13.65 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.28), residues: 972 helix: 1.17 (0.27), residues: 390 sheet: 0.54 (0.42), residues: 155 loop : 0.02 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 559 TYR 0.017 0.001 TYR E 351 PHE 0.019 0.002 PHE H 64 TRP 0.029 0.001 TRP H 47 HIS 0.005 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7199) covalent geometry : angle 0.53312 ( 9861) SS BOND : bond 0.00690 ( 9) SS BOND : angle 1.78403 ( 18) hydrogen bonds : bond 0.04340 ( 363) hydrogen bonds : angle 4.63519 ( 993) link_ALPHA1-6 : bond 0.00633 ( 1) link_ALPHA1-6 : angle 1.36879 ( 3) link_BETA1-4 : bond 0.00461 ( 2) link_BETA1-4 : angle 1.81997 ( 6) link_BETA1-6 : bond 0.00140 ( 1) link_BETA1-6 : angle 1.34616 ( 3) link_NAG-ASN : bond 0.00370 ( 6) link_NAG-ASN : angle 1.93162 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.13 seconds wall clock time: 38 minutes 53.11 seconds (2333.11 seconds total)