Starting phenix.real_space_refine on Sun May 11 01:26:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s9g_40240/05_2025/8s9g_40240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9g_40240/05_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_40240/05_2025/8s9g_40240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9g_40240/05_2025/8s9g_40240.map" model { file = "/net/cci-nas-00/data/ceres_data/8s9g_40240/05_2025/8s9g_40240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9g_40240/05_2025/8s9g_40240.cif" } resolution = 3.0 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= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 16, 'HIS:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 1, 'GLU:plan': 32, 'ARG:plan': 3} 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: {'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} 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, 'ASP:plan': 4, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} 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: 5.36, per 1000 atoms: 0.77 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: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.82 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: 2.30 Time building geometry restraints manager: 2.33 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- 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 (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: -0.22 (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 TRP 0.017 0.004 TRP H 117 HIS 0.005 0.001 HIS A 241 PHE 0.019 0.003 PHE A 32 TYR 0.025 0.004 TYR A 41 ARG 0.006 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.05256 ( 6) link_NAG-ASN : angle 8.14650 ( 18) 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) hydrogen bonds : bond 0.21910 ( 363) hydrogen bonds : angle 7.08183 ( 993) link_BETA1-6 : bond 0.04779 ( 1) link_BETA1-6 : angle 2.25770 ( 3) SS BOND : bond 0.04792 ( 9) SS BOND : angle 3.61559 ( 18) covalent geometry : bond 0.00979 ( 7199) covalent geometry : angle 1.29210 ( 9861) *********************** 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 : 0.662 Fit side-chains revert: symmetry clash REVERT: E 453 TYR cc_start: 0.7135 (p90) cc_final: 0.6899 (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: 0.9929 time to fit residues: 103.7084 Evaluate side-chains 61 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 81 optimal weight: 1.9990 chunk 73 optimal weight: 0.0060 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 417 ASN E 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.215979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.192302 restraints weight = 6707.160| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.50 r_work: 0.3957 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7218 Z= 0.155 Angle : 0.652 13.798 9909 Z= 0.329 Chirality : 0.044 0.222 1096 Planarity : 0.005 0.046 1280 Dihedral : 7.197 68.638 1264 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.48 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 (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: 0.72 (0.27), residues: 972 helix: 0.74 (0.26), residues: 382 sheet: 0.39 (0.40), residues: 152 loop : 0.46 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 117 HIS 0.004 0.001 HIS E 505 PHE 0.017 0.002 PHE A 314 TYR 0.019 0.002 TYR A 385 ARG 0.005 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 6) link_NAG-ASN : angle 5.12534 ( 18) link_ALPHA1-6 : bond 0.00532 ( 1) link_ALPHA1-6 : angle 1.83760 ( 3) link_BETA1-4 : bond 0.00747 ( 2) link_BETA1-4 : angle 2.99675 ( 6) hydrogen bonds : bond 0.05581 ( 363) hydrogen bonds : angle 5.16357 ( 993) link_BETA1-6 : bond 0.00364 ( 1) link_BETA1-6 : angle 1.27413 ( 3) SS BOND : bond 0.00631 ( 9) SS BOND : angle 1.26154 ( 18) covalent geometry : bond 0.00327 ( 7199) covalent geometry : angle 0.60769 ( 9861) *********************** 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 83 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 53 ASN cc_start: 0.4055 (OUTLIER) cc_final: 0.3671 (m-40) REVERT: A 97 LEU cc_start: 0.7258 (tp) cc_final: 0.6740 (tp) REVERT: H 90 ASP cc_start: 0.5861 (m-30) cc_final: 0.5564 (m-30) REVERT: L 55 ARG cc_start: 0.7339 (ttm110) cc_final: 0.6901 (mtm110) outliers start: 9 outliers final: 3 residues processed: 79 average time/residue: 0.9146 time to fit residues: 77.9225 Evaluate side-chains 66 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 83 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS E 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.212203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.189200 restraints weight = 6860.221| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.52 r_work: 0.3940 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 7218 Z= 0.151 Angle : 0.600 12.072 9909 Z= 0.303 Chirality : 0.043 0.291 1096 Planarity : 0.004 0.036 1280 Dihedral : 5.705 44.138 1264 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.44 % Allowed : 9.78 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.83 (0.27), residues: 972 helix: 0.95 (0.27), residues: 374 sheet: 0.42 (0.41), residues: 152 loop : 0.42 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS E 505 PHE 0.016 0.002 PHE E 429 TYR 0.017 0.002 TYR E 495 ARG 0.004 0.000 ARG A 393 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 6) link_NAG-ASN : angle 3.93963 ( 18) link_ALPHA1-6 : bond 0.00731 ( 1) link_ALPHA1-6 : angle 1.69245 ( 3) link_BETA1-4 : bond 0.00594 ( 2) link_BETA1-4 : angle 2.69788 ( 6) hydrogen bonds : bond 0.05085 ( 363) hydrogen bonds : angle 4.96174 ( 993) link_BETA1-6 : bond 0.00284 ( 1) link_BETA1-6 : angle 1.35749 ( 3) SS BOND : bond 0.00715 ( 9) SS BOND : angle 2.56094 ( 18) covalent geometry : bond 0.00340 ( 7199) covalent geometry : angle 0.56171 ( 9861) *********************** 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 84 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 53 ASN cc_start: 0.4236 (OUTLIER) cc_final: 0.3672 (m110) REVERT: A 97 LEU cc_start: 0.7226 (tp) cc_final: 0.6814 (tp) REVERT: A 249 MET cc_start: 0.5979 (mtp) cc_final: 0.5777 (mtp) REVERT: E 508 TYR cc_start: 0.8263 (m-80) cc_final: 0.8046 (m-80) REVERT: H 38 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6337 (ttp-170) REVERT: H 90 ASP cc_start: 0.5737 (m-30) cc_final: 0.5521 (m-30) REVERT: L 55 ARG cc_start: 0.7564 (ttm110) cc_final: 0.7091 (mtm110) outliers start: 12 outliers final: 4 residues processed: 81 average time/residue: 0.8985 time to fit residues: 78.3628 Evaluate side-chains 66 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 59 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 6 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.209342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.186313 restraints weight = 6783.632| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.47 r_work: 0.3907 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 7218 Z= 0.147 Angle : 0.586 10.071 9909 Z= 0.293 Chirality : 0.042 0.267 1096 Planarity : 0.004 0.041 1280 Dihedral : 5.084 41.741 1264 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.05 % Allowed : 10.18 % 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 (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: 0.79 (0.27), residues: 972 helix: 0.98 (0.27), residues: 375 sheet: 0.52 (0.41), residues: 153 loop : 0.28 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.004 0.001 HIS A 241 PHE 0.014 0.002 PHE E 429 TYR 0.015 0.002 TYR E 495 ARG 0.003 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 6) link_NAG-ASN : angle 3.54105 ( 18) link_ALPHA1-6 : bond 0.00465 ( 1) link_ALPHA1-6 : angle 1.68098 ( 3) link_BETA1-4 : bond 0.00487 ( 2) link_BETA1-4 : angle 2.55565 ( 6) hydrogen bonds : bond 0.04830 ( 363) hydrogen bonds : angle 4.87647 ( 993) link_BETA1-6 : bond 0.00087 ( 1) link_BETA1-6 : angle 1.34773 ( 3) SS BOND : bond 0.00667 ( 9) SS BOND : angle 2.19377 ( 18) covalent geometry : bond 0.00334 ( 7199) covalent geometry : angle 0.55512 ( 9861) *********************** 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 81 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7333 (tp) cc_final: 0.6873 (tp) REVERT: A 249 MET cc_start: 0.6215 (mtp) cc_final: 0.5933 (mtp) REVERT: H 38 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6504 (ttp-170) REVERT: H 90 ASP cc_start: 0.5849 (m-30) cc_final: 0.5581 (m-30) REVERT: L 55 ARG cc_start: 0.7604 (ttm110) cc_final: 0.7124 (mtm110) outliers start: 15 outliers final: 6 residues processed: 76 average time/residue: 0.9239 time to fit residues: 75.5399 Evaluate side-chains 67 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 210 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 = 0.4293 r_free = 0.4293 target = 0.209302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.185907 restraints weight = 6849.037| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.52 r_work: 0.3900 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 7218 Z= 0.149 Angle : 0.579 12.348 9909 Z= 0.293 Chirality : 0.042 0.277 1096 Planarity : 0.004 0.043 1280 Dihedral : 4.678 41.199 1264 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.05 % Allowed : 10.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 972 helix: 1.05 (0.27), residues: 370 sheet: 0.60 (0.41), residues: 149 loop : 0.16 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.002 PHE A 308 TYR 0.015 0.002 TYR A 385 ARG 0.003 0.000 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 6) link_NAG-ASN : angle 2.48546 ( 18) link_ALPHA1-6 : bond 0.00515 ( 1) link_ALPHA1-6 : angle 1.49239 ( 3) link_BETA1-4 : bond 0.00492 ( 2) link_BETA1-4 : angle 2.32159 ( 6) hydrogen bonds : bond 0.04808 ( 363) hydrogen bonds : angle 4.83515 ( 993) link_BETA1-6 : bond 0.00118 ( 1) link_BETA1-6 : angle 1.38420 ( 3) SS BOND : bond 0.00991 ( 9) SS BOND : angle 2.33276 ( 18) covalent geometry : bond 0.00339 ( 7199) covalent geometry : angle 0.55801 ( 9861) *********************** 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 82 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7279 (tp) cc_final: 0.6807 (tp) REVERT: E 508 TYR cc_start: 0.8209 (m-80) cc_final: 0.7976 (m-80) REVERT: H 38 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6469 (ttp-170) REVERT: H 90 ASP cc_start: 0.5891 (m-30) cc_final: 0.5635 (m-30) REVERT: L 55 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7124 (mtm110) outliers start: 15 outliers final: 7 residues processed: 79 average time/residue: 0.9122 time to fit residues: 77.5645 Evaluate side-chains 65 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 487 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 74 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 210 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 = 0.4286 r_free = 0.4286 target = 0.208441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184246 restraints weight = 6936.943| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.57 r_work: 0.3874 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7218 Z= 0.153 Angle : 0.581 10.146 9909 Z= 0.294 Chirality : 0.042 0.246 1096 Planarity : 0.004 0.044 1280 Dihedral : 4.654 41.142 1264 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.28 % Allowed : 10.18 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.54 (0.27), residues: 972 helix: 0.79 (0.26), residues: 391 sheet: 0.42 (0.41), residues: 155 loop : 0.09 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.002 PHE A 308 TYR 0.016 0.002 TYR A 385 ARG 0.003 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 6) link_NAG-ASN : angle 2.30777 ( 18) link_ALPHA1-6 : bond 0.00571 ( 1) link_ALPHA1-6 : angle 1.38560 ( 3) link_BETA1-4 : bond 0.00385 ( 2) link_BETA1-4 : angle 2.13788 ( 6) hydrogen bonds : bond 0.04829 ( 363) hydrogen bonds : angle 4.81771 ( 993) link_BETA1-6 : bond 0.00018 ( 1) link_BETA1-6 : angle 1.39229 ( 3) SS BOND : bond 0.00697 ( 9) SS BOND : angle 2.12059 ( 18) covalent geometry : bond 0.00348 ( 7199) covalent geometry : angle 0.56287 ( 9861) *********************** 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 82 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7267 (tp) cc_final: 0.6790 (tp) REVERT: A 247 LYS cc_start: 0.5931 (mtpt) cc_final: 0.5521 (pptt) REVERT: A 531 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6623 (mt0) REVERT: E 410 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7342 (mm) REVERT: E 508 TYR cc_start: 0.8237 (m-80) cc_final: 0.8017 (m-80) REVERT: H 38 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6410 (ttp-170) REVERT: H 90 ASP cc_start: 0.5836 (m-30) cc_final: 0.5567 (m-30) REVERT: L 55 ARG cc_start: 0.7570 (ttm110) cc_final: 0.7311 (mtt90) outliers start: 21 outliers final: 9 residues processed: 79 average time/residue: 0.8945 time to fit residues: 76.1857 Evaluate side-chains 70 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 487 VAL Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 410 ILE 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 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 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** A 210 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 = 0.4305 r_free = 0.4305 target = 0.210453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.184212 restraints weight = 6775.817| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.58 r_work: 0.3902 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 7218 Z= 0.125 Angle : 0.554 13.140 9909 Z= 0.278 Chirality : 0.041 0.271 1096 Planarity : 0.004 0.057 1280 Dihedral : 4.428 40.378 1264 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.05 % Allowed : 11.61 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 972 helix: 1.01 (0.26), residues: 390 sheet: 0.43 (0.41), residues: 156 loop : 0.09 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.004 0.001 HIS E 505 PHE 0.014 0.001 PHE A 315 TYR 0.019 0.001 TYR E 351 ARG 0.010 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 6) link_NAG-ASN : angle 2.11726 ( 18) link_ALPHA1-6 : bond 0.00660 ( 1) link_ALPHA1-6 : angle 1.39407 ( 3) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 1.97785 ( 6) hydrogen bonds : bond 0.04402 ( 363) hydrogen bonds : angle 4.68871 ( 993) link_BETA1-6 : bond 0.00089 ( 1) link_BETA1-6 : angle 1.34304 ( 3) SS BOND : bond 0.00930 ( 9) SS BOND : angle 2.24407 ( 18) covalent geometry : bond 0.00275 ( 7199) covalent geometry : angle 0.53649 ( 9861) *********************** 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 77 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7220 (tp) cc_final: 0.6767 (tp) REVERT: A 270 MET cc_start: 0.6897 (mmt) cc_final: 0.6599 (tpt) REVERT: E 410 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7312 (mm) REVERT: E 508 TYR cc_start: 0.8226 (m-80) cc_final: 0.8016 (m-80) REVERT: H 38 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6370 (ttp-170) REVERT: H 90 ASP cc_start: 0.5782 (m-30) cc_final: 0.5512 (m-30) REVERT: L 55 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7320 (mtt90) outliers start: 15 outliers final: 9 residues processed: 76 average time/residue: 0.8638 time to fit residues: 71.0375 Evaluate side-chains 70 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 487 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 410 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 13 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 210 ASN E 474 GLN E 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.207093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.182574 restraints weight = 6844.587| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.57 r_work: 0.3878 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7218 Z= 0.155 Angle : 0.581 12.962 9909 Z= 0.295 Chirality : 0.042 0.258 1096 Planarity : 0.005 0.049 1280 Dihedral : 4.584 40.965 1264 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.05 % Allowed : 11.81 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.54 (0.27), residues: 972 helix: 0.89 (0.26), residues: 391 sheet: 0.40 (0.41), residues: 154 loop : -0.02 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 HIS 0.005 0.001 HIS A 34 PHE 0.015 0.002 PHE A 315 TYR 0.016 0.002 TYR E 453 ARG 0.010 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 6) link_NAG-ASN : angle 2.15283 ( 18) link_ALPHA1-6 : bond 0.00670 ( 1) link_ALPHA1-6 : angle 1.35899 ( 3) link_BETA1-4 : bond 0.00446 ( 2) link_BETA1-4 : angle 1.94180 ( 6) hydrogen bonds : bond 0.04825 ( 363) hydrogen bonds : angle 4.79026 ( 993) link_BETA1-6 : bond 0.00026 ( 1) link_BETA1-6 : angle 1.40393 ( 3) SS BOND : bond 0.00811 ( 9) SS BOND : angle 2.11860 ( 18) covalent geometry : bond 0.00354 ( 7199) covalent geometry : angle 0.56437 ( 9861) *********************** 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 74 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7255 (tp) cc_final: 0.6788 (tp) REVERT: A 247 LYS cc_start: 0.5949 (mtpt) cc_final: 0.5576 (pptt) REVERT: A 270 MET cc_start: 0.6952 (mmt) cc_final: 0.6610 (tpt) REVERT: E 410 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7478 (mm) REVERT: H 38 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6394 (ttp-170) REVERT: H 90 ASP cc_start: 0.5846 (m-30) cc_final: 0.5589 (m-30) REVERT: L 55 ARG cc_start: 0.7559 (ttm110) cc_final: 0.7285 (mtt90) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.9025 time to fit residues: 71.1083 Evaluate side-chains 70 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 487 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 410 ILE 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 0 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 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 = 0.4300 r_free = 0.4300 target = 0.209565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186401 restraints weight = 6905.892| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.49 r_work: 0.3914 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7218 Z= 0.129 Angle : 0.548 12.615 9909 Z= 0.278 Chirality : 0.041 0.251 1096 Planarity : 0.004 0.047 1280 Dihedral : 4.457 40.407 1264 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.26 % Allowed : 11.81 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.63 (0.27), residues: 972 helix: 1.04 (0.26), residues: 390 sheet: 0.35 (0.40), residues: 156 loop : -0.01 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 47 HIS 0.004 0.001 HIS E 505 PHE 0.015 0.002 PHE A 315 TYR 0.017 0.001 TYR E 351 ARG 0.009 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 6) link_NAG-ASN : angle 2.03420 ( 18) link_ALPHA1-6 : bond 0.00595 ( 1) link_ALPHA1-6 : angle 1.32462 ( 3) link_BETA1-4 : bond 0.00408 ( 2) link_BETA1-4 : angle 1.87647 ( 6) hydrogen bonds : bond 0.04437 ( 363) hydrogen bonds : angle 4.68462 ( 993) link_BETA1-6 : bond 0.00089 ( 1) link_BETA1-6 : angle 1.38319 ( 3) SS BOND : bond 0.00731 ( 9) SS BOND : angle 1.90643 ( 18) covalent geometry : bond 0.00287 ( 7199) covalent geometry : angle 0.53333 ( 9861) *********************** 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 78 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7267 (tp) cc_final: 0.6805 (tp) REVERT: A 247 LYS cc_start: 0.5990 (mtpt) cc_final: 0.5556 (pptt) REVERT: A 270 MET cc_start: 0.6829 (mmt) cc_final: 0.6576 (tpt) REVERT: E 410 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7452 (mm) REVERT: H 38 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6389 (ttp-170) REVERT: H 90 ASP cc_start: 0.5889 (m-30) cc_final: 0.5637 (m-30) REVERT: L 55 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7341 (mtt90) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.9680 time to fit residues: 80.6401 Evaluate side-chains 74 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 487 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 410 ILE 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 81 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 0.0470 chunk 77 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 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 = 0.4313 r_free = 0.4313 target = 0.211482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.188552 restraints weight = 6825.280| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.53 r_work: 0.3930 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 7218 Z= 0.108 Angle : 0.517 12.433 9909 Z= 0.262 Chirality : 0.041 0.238 1096 Planarity : 0.004 0.048 1280 Dihedral : 4.265 39.466 1264 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.85 % Allowed : 12.63 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.86 (0.28), residues: 972 helix: 1.32 (0.27), residues: 384 sheet: 0.45 (0.41), residues: 156 loop : 0.05 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.005 0.001 HIS E 505 PHE 0.020 0.001 PHE H 64 TYR 0.018 0.001 TYR E 351 ARG 0.009 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 6) link_NAG-ASN : angle 1.87274 ( 18) link_ALPHA1-6 : bond 0.00600 ( 1) link_ALPHA1-6 : angle 1.36600 ( 3) link_BETA1-4 : bond 0.00422 ( 2) link_BETA1-4 : angle 1.78408 ( 6) hydrogen bonds : bond 0.04032 ( 363) hydrogen bonds : angle 4.54637 ( 993) link_BETA1-6 : bond 0.00134 ( 1) link_BETA1-6 : angle 1.33617 ( 3) SS BOND : bond 0.00652 ( 9) SS BOND : angle 1.75914 ( 18) covalent geometry : bond 0.00232 ( 7199) covalent geometry : angle 0.50368 ( 9861) ********************** 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 81 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7172 (tp) cc_final: 0.6741 (tp) REVERT: A 270 MET cc_start: 0.6837 (mmt) cc_final: 0.6556 (tpt) REVERT: E 410 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7418 (mm) REVERT: H 38 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6343 (ttp-170) REVERT: H 90 ASP cc_start: 0.5788 (m-30) cc_final: 0.5535 (m-30) REVERT: L 55 ARG cc_start: 0.7606 (ttm110) cc_final: 0.7350 (mtt90) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 0.8973 time to fit residues: 75.5055 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 : 0.644 ------------------------------------------------------------------------------- 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 408 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 410 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 68 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 69 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 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 = 0.4307 r_free = 0.4307 target = 0.211278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.184632 restraints weight = 6841.661| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 1.61 r_work: 0.3913 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3797 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= 0.124 Angle : 0.548 12.326 9909 Z= 0.279 Chirality : 0.041 0.240 1096 Planarity : 0.004 0.047 1280 Dihedral : 4.340 40.698 1264 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.24 % Allowed : 14.05 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.28), residues: 972 helix: 1.26 (0.27), residues: 390 sheet: 0.48 (0.41), residues: 156 loop : 0.05 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 47 HIS 0.006 0.001 HIS A 34 PHE 0.022 0.002 PHE H 64 TYR 0.016 0.001 TYR E 351 ARG 0.008 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 6) link_NAG-ASN : angle 1.91658 ( 18) link_ALPHA1-6 : bond 0.00589 ( 1) link_ALPHA1-6 : angle 1.34300 ( 3) link_BETA1-4 : bond 0.00423 ( 2) link_BETA1-4 : angle 1.79342 ( 6) hydrogen bonds : bond 0.04243 ( 363) hydrogen bonds : angle 4.59630 ( 993) link_BETA1-6 : bond 0.00149 ( 1) link_BETA1-6 : angle 1.36130 ( 3) SS BOND : bond 0.00696 ( 9) SS BOND : angle 1.79216 ( 18) covalent geometry : bond 0.00274 ( 7199) covalent geometry : angle 0.53502 ( 9861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4387.90 seconds wall clock time: 76 minutes 17.44 seconds (4577.44 seconds total)