Starting phenix.real_space_refine on Thu Jul 2 06:23:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8s9g_40240/07_2026/8s9g_40240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9g_40240/07_2026/8s9g_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 { model { file = "/net/cci-nas-00/data/ceres_data/8s9g_40240/07_2026/8s9g_40240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9g_40240/07_2026/8s9g_40240.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8s9g_40240/07_2026/8s9g_40240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8s9g_40240/07_2026/8s9g_40240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s9g_40240/07_2026/8s9g_40240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9g_40240/07_2026/8s9g_40240.map" } 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-dev-6108/lib/python3.11/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 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 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 chiralities: 1 Time building chain proxies: 1.09, per 1000 atoms: 0.16 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: 0.59 Conformation dependent library (CDL) restraints added in 364.7 milliseconds 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: 0.15 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: 0.89 Time building geometry restraints manager: 0.76 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 - 16.25: 3869 16.25 - 32.49: 125 32.49 - 48.74: 33 48.74 - 64.99: 13 64.99 - 81.23: 4 Dihedral angle restraints: 4044 sinusoidal: 1184 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=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -113.98 27.98 1 1.00e+01 1.00e-02 1.12e+01 dihedral pdb=" CA SER E 494 " pdb=" C SER E 494 " pdb=" N TYR E 495 " pdb=" CA TYR E 495 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 4041 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: 1.340 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.560 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 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 : 10.207 81.232 2187 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 are 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/Z covalent geometry : bond 0.00979 / 0.56 ( 7199) covalent geometry : angle 1.29210 / 0.90 ( 9861) SS BOND : bond 0.04792 / 3.18 ( 9) SS BOND : angle 3.61559 / 2.30 ( 18) hydrogen bonds : bond 0.21910 / 14.39 ( 363) hydrogen bonds : angle 7.08183 / 5.26 ( 993) link_ALPHA1-6 : bond 0.05456 / 2.87 ( 1) link_ALPHA1-6 : angle 1.62842 / 0.86 ( 3) link_BETA1-4 : bond 0.05840 / 2.90 ( 2) link_BETA1-4 : angle 3.35659 / 1.82 ( 6) link_BETA1-6 : bond 0.04779 / 2.52 ( 1) link_BETA1-6 : angle 2.25770 / 1.20 ( 3) link_NAG-ASN : bond 0.05256 / 2.97 ( 6) link_NAG-ASN : angle 8.14650 / 4.25 ( 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 : 0.168 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: 0.3854 time to fit residues: 40.1331 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 : 0.160 ------------------------------------------------------------------------------- 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... A 417 HIS E 474 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.217729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.195456 restraints weight = 6824.264| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 1.48 r_work: 0.3996 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7218 Z= 0.143 Angle : 0.624 13.665 9909 Z= 0.319 Chirality : 0.042 0.206 1096 Planarity : 0.004 0.043 1280 Dihedral : 4.283 39.414 1062 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.83 % Allowed : 8.35 % Favored : 89.82 % 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 are not related in a simple way. whole: 0.78 (0.27), residues: 972 helix: 0.83 (0.26), residues: 382 sheet: 0.38 (0.40), residues: 152 loop : 0.48 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 559 TYR 0.018 0.002 TYR A 516 PHE 0.016 0.002 PHE A 314 TRP 0.011 0.001 TRP H 117 HIS 0.004 0.001 HIS E 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 7199) covalent geometry : angle 0.58549 / 0.31 ( 9861) SS BOND : bond 0.00337 / 0.21 ( 9) SS BOND : angle 1.76944 / 1.22 ( 18) hydrogen bonds : bond 0.05555 / 3.80 ( 363) hydrogen bonds : angle 5.14831 / 3.82 ( 993) link_ALPHA1-6 : bond 0.00696 / 0.37 ( 1) link_ALPHA1-6 : angle 1.37565 / 0.64 ( 3) link_BETA1-4 : bond 0.00396 / 0.19 ( 2) link_BETA1-4 : angle 2.29403 / 1.17 ( 6) link_BETA1-6 : bond 0.00189 / 0.10 ( 1) link_BETA1-6 : angle 1.24500 / 0.65 ( 3) link_NAG-ASN : bond 0.00431 / 0.27 ( 6) link_NAG-ASN : angle 4.61753 / 2.80 ( 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 82 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 53 ASN cc_start: 0.3985 (OUTLIER) cc_final: 0.3623 (m-40) REVERT: A 97 LEU cc_start: 0.7227 (tp) cc_final: 0.6721 (tp) REVERT: A 247 LYS cc_start: 0.6037 (mmtt) cc_final: 0.5691 (pptt) REVERT: A 249 MET cc_start: 0.5910 (mtp) cc_final: 0.5655 (mpm) REVERT: H 90 ASP cc_start: 0.5794 (m-30) cc_final: 0.5502 (m-30) REVERT: L 55 ARG cc_start: 0.7276 (ttm110) cc_final: 0.6849 (mtm110) outliers start: 9 outliers final: 3 residues processed: 78 average time/residue: 0.3290 time to fit residues: 27.5256 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 : 0.202 ------------------------------------------------------------------------------- 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: 3.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 79 optimal weight: 0.2980 chunk 29 optimal weight: 0.0470 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS A 210 ASN 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 = 0.4348 r_free = 0.4348 target = 0.215575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.192875 restraints weight = 6772.058| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.50 r_work: 0.3961 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 7218 Z= 0.131 Angle : 0.566 12.138 9909 Z= 0.286 Chirality : 0.041 0.259 1096 Planarity : 0.004 0.035 1280 Dihedral : 4.039 41.405 1062 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.65 % Allowed : 9.78 % Favored : 87.58 % 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 are not related in a simple way. whole: 1.03 (0.27), residues: 972 helix: 1.13 (0.27), residues: 375 sheet: 0.54 (0.42), residues: 142 loop : 0.51 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.015 0.002 TYR A 521 PHE 0.014 0.002 PHE L 98 TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7199) covalent geometry : angle 0.52821 / 0.28 ( 9861) SS BOND : bond 0.00826 / 0.56 ( 9) SS BOND : angle 2.24658 / 1.52 ( 18) hydrogen bonds : bond 0.04886 / 3.33 ( 363) hydrogen bonds : angle 4.85269 / 3.58 ( 993) link_ALPHA1-6 : bond 0.00691 / 0.36 ( 1) link_ALPHA1-6 : angle 1.30202 / 0.67 ( 3) link_BETA1-4 : bond 0.00578 / 0.29 ( 2) link_BETA1-4 : angle 1.81942 / 0.96 ( 6) link_BETA1-6 : bond 0.00195 / 0.10 ( 1) link_BETA1-6 : angle 1.25712 / 0.64 ( 3) link_NAG-ASN : bond 0.00402 / 0.23 ( 6) link_NAG-ASN : angle 4.07018 / 2.36 ( 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 85 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.4070 (OUTLIER) cc_final: 0.3719 (m110) REVERT: A 97 LEU cc_start: 0.7123 (tp) cc_final: 0.6723 (tp) REVERT: A 247 LYS cc_start: 0.6049 (mmtt) cc_final: 0.5585 (pptt) REVERT: H 38 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6317 (ttp-170) REVERT: H 90 ASP cc_start: 0.5710 (m-30) cc_final: 0.5458 (m-30) REVERT: L 55 ARG cc_start: 0.7353 (ttm110) cc_final: 0.6931 (mtm110) outliers start: 13 outliers final: 2 residues processed: 81 average time/residue: 0.3303 time to fit residues: 28.7769 Evaluate side-chains 68 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 H residue 38 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 47 optimal weight: 0.0040 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN E 417 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 = 0.4322 r_free = 0.4322 target = 0.212433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.189245 restraints weight = 6951.636| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.54 r_work: 0.3933 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 7218 Z= 0.137 Angle : 0.569 10.865 9909 Z= 0.285 Chirality : 0.041 0.268 1096 Planarity : 0.004 0.040 1280 Dihedral : 4.054 41.919 1062 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.27), residues: 972 helix: 1.19 (0.27), residues: 375 sheet: 0.73 (0.42), residues: 143 loop : 0.34 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.016 0.002 TYR E 453 PHE 0.016 0.002 PHE E 377 TRP 0.016 0.001 TRP H 47 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7199) covalent geometry : angle 0.53747 / 0.28 ( 9861) SS BOND : bond 0.00683 / 0.46 ( 9) SS BOND : angle 2.21911 / 1.50 ( 18) hydrogen bonds : bond 0.04652 / 3.19 ( 363) hydrogen bonds : angle 4.74974 / 3.51 ( 993) link_ALPHA1-6 : bond 0.00595 / 0.31 ( 1) link_ALPHA1-6 : angle 1.33231 / 0.68 ( 3) link_BETA1-4 : bond 0.00584 / 0.29 ( 2) link_BETA1-4 : angle 1.74284 / 0.92 ( 6) link_BETA1-6 : bond 0.00223 / 0.12 ( 1) link_BETA1-6 : angle 1.29380 / 0.66 ( 3) link_NAG-ASN : bond 0.00315 / 0.17 ( 6) link_NAG-ASN : angle 3.65447 / 2.11 ( 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 86 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 53 ASN cc_start: 0.4144 (OUTLIER) cc_final: 0.3500 (m110) REVERT: A 97 LEU cc_start: 0.7303 (tp) cc_final: 0.6862 (tp) REVERT: A 247 LYS cc_start: 0.6149 (mmtt) cc_final: 0.5565 (pptt) REVERT: A 249 MET cc_start: 0.6439 (mtp) cc_final: 0.6026 (mtp) REVERT: H 38 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6488 (ttp-170) REVERT: H 90 ASP cc_start: 0.5733 (m-30) cc_final: 0.5430 (m-30) REVERT: L 55 ARG cc_start: 0.7572 (ttm110) cc_final: 0.7095 (mtm110) outliers start: 15 outliers final: 4 residues processed: 81 average time/residue: 0.3536 time to fit residues: 30.6526 Evaluate side-chains 68 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 65 optimal weight: 0.6980 chunk 30 optimal weight: 0.0050 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4317 r_free = 0.4317 target = 0.212435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.188742 restraints weight = 6746.131| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.59 r_work: 0.3945 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.2939 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= 0.116 Angle : 0.537 12.540 9909 Z= 0.269 Chirality : 0.040 0.276 1096 Planarity : 0.004 0.043 1280 Dihedral : 3.930 41.419 1062 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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 are not related in a simple way. whole: 1.20 (0.27), residues: 972 helix: 1.43 (0.27), residues: 369 sheet: 0.84 (0.43), residues: 141 loop : 0.38 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 355 TYR 0.014 0.001 TYR E 351 PHE 0.009 0.001 PHE A 315 TRP 0.017 0.001 TRP H 47 HIS 0.004 0.001 HIS E 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 7199) covalent geometry : angle 0.50969 / 0.26 ( 9861) SS BOND : bond 0.00841 / 0.57 ( 9) SS BOND : angle 2.00647 / 1.35 ( 18) hydrogen bonds : bond 0.04244 / 2.92 ( 363) hydrogen bonds : angle 4.62841 / 3.41 ( 993) link_ALPHA1-6 : bond 0.00603 / 0.32 ( 1) link_ALPHA1-6 : angle 1.32446 / 0.68 ( 3) link_BETA1-4 : bond 0.00470 / 0.23 ( 2) link_BETA1-4 : angle 1.60631 / 0.85 ( 6) link_BETA1-6 : bond 0.00206 / 0.11 ( 1) link_BETA1-6 : angle 1.24288 / 0.64 ( 3) link_NAG-ASN : bond 0.00298 / 0.17 ( 6) link_NAG-ASN : angle 3.27374 / 1.91 ( 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 77 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7306 (tp) cc_final: 0.6866 (tp) REVERT: A 247 LYS cc_start: 0.6205 (mmtt) cc_final: 0.5610 (pptt) REVERT: A 249 MET cc_start: 0.6519 (mtp) cc_final: 0.6135 (mtp) REVERT: E 508 TYR cc_start: 0.8232 (m-80) cc_final: 0.7957 (m-80) REVERT: H 38 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6404 (ttp-170) REVERT: H 90 ASP cc_start: 0.5732 (m-30) cc_final: 0.5424 (m-30) REVERT: L 55 ARG cc_start: 0.7504 (ttm110) cc_final: 0.7045 (mtm110) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 0.3257 time to fit residues: 26.1253 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.8980 chunk 61 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 26 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4311 r_free = 0.4311 target = 0.211663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.187780 restraints weight = 6785.430| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.58 r_work: 0.3935 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7218 Z= 0.121 Angle : 0.535 11.277 9909 Z= 0.270 Chirality : 0.041 0.246 1096 Planarity : 0.004 0.053 1280 Dihedral : 3.951 41.180 1062 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.44 % Allowed : 10.59 % Favored : 86.97 % 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 are not related in a simple way. whole: 1.10 (0.27), residues: 972 helix: 1.34 (0.27), residues: 377 sheet: 0.86 (0.43), residues: 141 loop : 0.30 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 559 TYR 0.016 0.001 TYR E 351 PHE 0.011 0.001 PHE A 315 TRP 0.020 0.001 TRP H 47 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7199) covalent geometry : angle 0.51846 / 0.27 ( 9861) SS BOND : bond 0.00629 / 0.42 ( 9) SS BOND : angle 1.95006 / 1.32 ( 18) hydrogen bonds : bond 0.04316 / 2.96 ( 363) hydrogen bonds : angle 4.60238 / 3.39 ( 993) link_ALPHA1-6 : bond 0.00655 / 0.34 ( 1) link_ALPHA1-6 : angle 1.39583 / 0.71 ( 3) link_BETA1-4 : bond 0.00448 / 0.22 ( 2) link_BETA1-4 : angle 1.60504 / 0.85 ( 6) link_BETA1-6 : bond 0.00165 / 0.09 ( 1) link_BETA1-6 : angle 1.24180 / 0.64 ( 3) link_NAG-ASN : bond 0.00319 / 0.19 ( 6) link_NAG-ASN : angle 2.21328 / 1.38 ( 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 76 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7174 (tp) cc_final: 0.6759 (tp) REVERT: A 247 LYS cc_start: 0.6272 (mmtt) cc_final: 0.5635 (pptt) REVERT: A 249 MET cc_start: 0.6530 (mtp) cc_final: 0.6159 (mtp) REVERT: E 508 TYR cc_start: 0.8211 (m-80) cc_final: 0.8002 (m-80) REVERT: H 38 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6380 (ttp-170) REVERT: H 90 ASP cc_start: 0.5725 (m-30) cc_final: 0.5416 (m-30) REVERT: L 55 ARG cc_start: 0.7560 (ttm110) cc_final: 0.7277 (mtt90) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.3593 time to fit residues: 28.1953 Evaluate side-chains 67 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 408 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 66 optimal weight: 0.0270 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4339 r_free = 0.4339 target = 0.214630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.191712 restraints weight = 6901.346| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.51 r_work: 0.3953 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 7218 Z= 0.110 Angle : 0.513 13.241 9909 Z= 0.262 Chirality : 0.040 0.243 1096 Planarity : 0.004 0.044 1280 Dihedral : 3.858 41.213 1062 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.04 % Allowed : 10.79 % 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 are not related in a simple way. whole: 1.20 (0.27), residues: 972 helix: 1.38 (0.27), residues: 384 sheet: 0.91 (0.43), residues: 141 loop : 0.38 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 559 TYR 0.016 0.001 TYR E 351 PHE 0.014 0.001 PHE A 315 TRP 0.020 0.001 TRP H 47 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7199) covalent geometry : angle 0.49723 / 0.26 ( 9861) SS BOND : bond 0.00661 / 0.45 ( 9) SS BOND : angle 1.88741 / 1.27 ( 18) hydrogen bonds : bond 0.04031 / 2.77 ( 363) hydrogen bonds : angle 4.51808 / 3.33 ( 993) link_ALPHA1-6 : bond 0.00609 / 0.32 ( 1) link_ALPHA1-6 : angle 1.35288 / 0.69 ( 3) link_BETA1-4 : bond 0.00419 / 0.21 ( 2) link_BETA1-4 : angle 1.53706 / 0.81 ( 6) link_BETA1-6 : bond 0.00008 / 0.00 ( 1) link_BETA1-6 : angle 1.17690 / 0.61 ( 3) link_NAG-ASN : bond 0.00421 / 0.24 ( 6) link_NAG-ASN : angle 2.11073 / 1.27 ( 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: 10 poor density : 63 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7088 (tp) cc_final: 0.6705 (tp) REVERT: A 247 LYS cc_start: 0.6276 (mmtt) cc_final: 0.5644 (pptt) REVERT: A 249 MET cc_start: 0.6531 (mtp) cc_final: 0.6233 (mtp) REVERT: H 38 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6322 (ttp-170) REVERT: H 64 PHE cc_start: 0.6636 (m-80) cc_final: 0.6431 (m-80) REVERT: H 90 ASP cc_start: 0.5720 (m-30) cc_final: 0.5450 (m-30) REVERT: L 55 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7230 (mtt90) REVERT: L 92 HIS cc_start: 0.7048 (t70) cc_final: 0.6744 (t70) outliers start: 10 outliers final: 6 residues processed: 71 average time/residue: 0.3401 time to fit residues: 25.9661 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 : 0.232 ------------------------------------------------------------------------------- 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 408 MET 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 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: 1.9990 chunk 75 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.0870 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 0.0370 chunk 15 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 0.0770 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4329 r_free = 0.4329 target = 0.213742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.190099 restraints weight = 6769.066| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.59 r_work: 0.3959 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 7218 Z= 0.105 Angle : 0.499 12.935 9909 Z= 0.255 Chirality : 0.040 0.236 1096 Planarity : 0.004 0.044 1280 Dihedral : 3.787 40.629 1062 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.83 % Allowed : 11.41 % 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 are not related in a simple way. whole: 1.25 (0.28), residues: 972 helix: 1.54 (0.27), residues: 383 sheet: 0.95 (0.43), residues: 141 loop : 0.28 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 559 TYR 0.015 0.001 TYR E 351 PHE 0.010 0.001 PHE A 315 TRP 0.020 0.001 TRP H 47 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7199) covalent geometry : angle 0.48409 / 0.25 ( 9861) SS BOND : bond 0.00679 / 0.46 ( 9) SS BOND : angle 1.85546 / 1.24 ( 18) hydrogen bonds : bond 0.03922 / 2.70 ( 363) hydrogen bonds : angle 4.44377 / 3.27 ( 993) link_ALPHA1-6 : bond 0.00580 / 0.31 ( 1) link_ALPHA1-6 : angle 1.34810 / 0.68 ( 3) link_BETA1-4 : bond 0.00448 / 0.22 ( 2) link_BETA1-4 : angle 1.50812 / 0.79 ( 6) link_BETA1-6 : bond 0.00230 / 0.12 ( 1) link_BETA1-6 : angle 1.23175 / 0.63 ( 3) link_NAG-ASN : bond 0.00331 / 0.19 ( 6) link_NAG-ASN : angle 2.05219 / 1.24 ( 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 74 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7102 (tp) cc_final: 0.6703 (tp) REVERT: A 247 LYS cc_start: 0.6279 (mmtt) cc_final: 0.5817 (pptt) REVERT: A 249 MET cc_start: 0.6565 (mtp) cc_final: 0.6263 (mtp) REVERT: H 38 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6326 (ttp-170) REVERT: H 90 ASP cc_start: 0.5631 (m-30) cc_final: 0.5346 (m-30) outliers start: 9 outliers final: 7 residues processed: 71 average time/residue: 0.3698 time to fit residues: 28.2490 Evaluate side-chains 71 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 408 MET 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 H residue 38 ARG Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4267 r_free = 0.4267 target = 0.206169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182151 restraints weight = 7017.229| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.57 r_work: 0.3858 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 7218 Z= 0.232 Angle : 0.674 13.458 9909 Z= 0.346 Chirality : 0.045 0.266 1096 Planarity : 0.005 0.056 1280 Dihedral : 4.486 44.069 1062 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.24 % Allowed : 11.81 % 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 are not related in a simple way. whole: 0.48 (0.27), residues: 972 helix: 0.67 (0.26), residues: 392 sheet: 0.69 (0.41), residues: 152 loop : -0.01 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 559 TYR 0.026 0.003 TYR E 508 PHE 0.021 0.003 PHE A 308 TRP 0.023 0.003 TRP H 47 HIS 0.011 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 ( 7199) covalent geometry : angle 0.65719 / 0.34 ( 9861) SS BOND : bond 0.01002 / 0.67 ( 9) SS BOND : angle 2.25624 / 1.51 ( 18) hydrogen bonds : bond 0.05706 / 3.89 ( 363) hydrogen bonds : angle 4.98362 / 3.67 ( 993) link_ALPHA1-6 : bond 0.00717 / 0.38 ( 1) link_ALPHA1-6 : angle 1.40210 / 0.70 ( 3) link_BETA1-4 : bond 0.00455 / 0.22 ( 2) link_BETA1-4 : angle 1.95721 / 1.06 ( 6) link_BETA1-6 : bond 0.00124 / 0.07 ( 1) link_BETA1-6 : angle 1.35453 / 0.70 ( 3) link_NAG-ASN : bond 0.00524 / 0.29 ( 6) link_NAG-ASN : angle 2.49139 / 1.52 ( 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: 11 poor density : 63 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7379 (tp) cc_final: 0.6908 (tp) REVERT: H 38 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6341 (ttp-170) REVERT: H 90 ASP cc_start: 0.5908 (m-30) cc_final: 0.5616 (m-30) outliers start: 11 outliers final: 7 residues processed: 73 average time/residue: 0.3152 time to fit residues: 24.8724 Evaluate side-chains 68 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 71 optimal weight: 0.0050 chunk 64 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4291 r_free = 0.4291 target = 0.208948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185373 restraints weight = 6805.998| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.54 r_work: 0.3911 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.3632 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= 0.136 Angle : 0.575 12.926 9909 Z= 0.293 Chirality : 0.042 0.248 1096 Planarity : 0.004 0.047 1280 Dihedral : 4.184 42.022 1062 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.83 % Allowed : 13.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.27), residues: 972 helix: 1.08 (0.26), residues: 384 sheet: 0.60 (0.41), residues: 151 loop : 0.00 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 559 TYR 0.015 0.002 TYR A 521 PHE 0.018 0.002 PHE H 64 TRP 0.027 0.002 TRP H 47 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7199) covalent geometry : angle 0.55990 / 0.29 ( 9861) SS BOND : bond 0.00739 / 0.50 ( 9) SS BOND : angle 1.93419 / 1.29 ( 18) hydrogen bonds : bond 0.04546 / 3.11 ( 363) hydrogen bonds : angle 4.77815 / 3.51 ( 993) link_ALPHA1-6 : bond 0.00692 / 0.36 ( 1) link_ALPHA1-6 : angle 1.36558 / 0.71 ( 3) link_BETA1-4 : bond 0.00478 / 0.24 ( 2) link_BETA1-4 : angle 1.69954 / 0.90 ( 6) link_BETA1-6 : bond 0.00178 / 0.09 ( 1) link_BETA1-6 : angle 1.26602 / 0.66 ( 3) link_NAG-ASN : bond 0.00419 / 0.25 ( 6) link_NAG-ASN : angle 2.24886 / 1.37 ( 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 69 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7284 (tp) cc_final: 0.6838 (tp) REVERT: H 38 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6501 (ttp-170) REVERT: H 90 ASP cc_start: 0.5750 (m-30) cc_final: 0.5493 (m-30) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.3693 time to fit residues: 27.1619 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 : 0.244 ------------------------------------------------------------------------------- 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 487 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain H residue 38 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4304 r_free = 0.4304 target = 0.210898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.184439 restraints weight = 6820.854| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.60 r_work: 0.3907 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3714 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= 0.131 Angle : 0.569 12.746 9909 Z= 0.288 Chirality : 0.041 0.243 1096 Planarity : 0.004 0.047 1280 Dihedral : 4.097 41.417 1062 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.22 % Allowed : 13.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.28), residues: 972 helix: 1.19 (0.27), residues: 384 sheet: 0.58 (0.41), residues: 157 loop : 0.01 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 559 TYR 0.015 0.002 TYR A 521 PHE 0.018 0.002 PHE H 64 TRP 0.027 0.001 TRP H 47 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7199) covalent geometry : angle 0.55495 / 0.28 ( 9861) SS BOND : bond 0.00725 / 0.49 ( 9) SS BOND : angle 1.85785 / 1.24 ( 18) hydrogen bonds : bond 0.04430 / 3.04 ( 363) hydrogen bonds : angle 4.71820 / 3.47 ( 993) link_ALPHA1-6 : bond 0.00700 / 0.37 ( 1) link_ALPHA1-6 : angle 1.36937 / 0.71 ( 3) link_BETA1-4 : bond 0.00452 / 0.22 ( 2) link_BETA1-4 : angle 1.62421 / 0.85 ( 6) link_BETA1-6 : bond 0.00189 / 0.10 ( 1) link_BETA1-6 : angle 1.26987 / 0.66 ( 3) link_NAG-ASN : bond 0.00376 / 0.22 ( 6) link_NAG-ASN : angle 2.15833 / 1.31 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.74 seconds wall clock time: 30 minutes 15.21 seconds (1815.21 seconds total)