Starting phenix.real_space_refine on Thu Jul 2 13:53:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hbf_34627/07_2026/8hbf_34627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbf_34627/07_2026/8hbf_34627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hbf_34627/07_2026/8hbf_34627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbf_34627/07_2026/8hbf_34627.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hbf_34627/07_2026/8hbf_34627.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hbf_34627/07_2026/8hbf_34627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hbf_34627/07_2026/8hbf_34627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbf_34627/07_2026/8hbf_34627.map" } resolution = 3.1 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= -0.002 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5438 2.51 5 N 1434 2.21 5 O 1511 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s 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: 8448 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3894 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 9 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 15, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 4444 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 573, 4442 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 101 Conformer: "B" Number of residues, atoms: 573, 4442 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 101 bond proxies already assigned to first conformer: 4530 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' NO': 1, 'GZO': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.66, per 1000 atoms: 0.31 Number of scatterers: 8448 At special positions: 0 Unit cell: (65.835, 107.635, 150.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 1 26.01 S 58 16.00 P 3 15.00 Mg 2 11.99 F 1 9.00 O 1511 8.00 N 1434 7.00 C 5438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 468.5 milliseconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 50.1% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.674A pdb=" N LEU A 74 " --> pdb=" O TYR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.628A pdb=" N GLN A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 128 through 149 removed outlier: 3.787A pdb=" N ILE A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.665A pdb=" N VAL A 154 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.716A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.763A pdb=" N LEU A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.778A pdb=" N TYR A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 404 through 407 Processing helix chain 'A' and resid 408 through 458 removed outlier: 3.719A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 498 through 521 removed outlier: 3.783A pdb=" N ARG A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 561 removed outlier: 4.122A pdb=" N ASP A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.728A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.839A pdb=" N LEU A 642 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 18 removed outlier: 4.167A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.861A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 removed outlier: 3.944A pdb=" N LYS B 72 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 removed outlier: 3.752A pdb=" N LEU B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 144 through 159 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.545A pdb=" N ARG B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.661A pdb=" N VAL B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 253' Processing helix chain 'B' and resid 264 through 271 removed outlier: 3.856A pdb=" N HIS B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.535A pdb=" N ARG B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 398 removed outlier: 3.566A pdb=" N GLU B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 408 removed outlier: 4.004A pdb=" N GLU B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 441 through 461 removed outlier: 3.756A pdb=" N THR B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 507 removed outlier: 3.530A pdb=" N SER B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.777A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 193 removed outlier: 3.841A pdb=" N HIS A 201 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.775A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 526 removed outlier: 7.155A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 523 through 526 removed outlier: 7.155A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 633 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.677A pdb=" N GLU B 182 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.615A pdb=" N ARG B 279 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU B 256 " --> pdb=" O ARG B 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 470 through 473 removed outlier: 7.025A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 473 removed outlier: 7.025A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASN B 563 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N MET B 599 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 601 " --> pdb=" O ARG B 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 511 through 512 510 hydrogen bonds defined for protein. 1458 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: 1.38 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 2763 1.36 - 1.55: 5755 1.55 - 1.73: 8 1.73 - 1.91: 91 1.91 - 2.09: 3 Bond restraints: 8620 Sorted by residual: bond pdb=" C13 GZO B 702 " pdb=" N06 GZO B 702 " ideal model delta sigma weight residual 1.327 1.535 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C17 GZO B 702 " pdb=" N07 GZO B 702 " ideal model delta sigma weight residual 1.322 1.476 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C17 GZO B 702 " pdb=" N08 GZO B 702 " ideal model delta sigma weight residual 1.321 1.473 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C12 GZO B 702 " pdb=" C18 GZO B 702 " ideal model delta sigma weight residual 1.397 1.536 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C25 GZO B 702 " pdb=" N06 GZO B 702 " ideal model delta sigma weight residual 1.319 1.456 -0.137 2.00e-02 2.50e+03 4.66e+01 ... (remaining 8615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 11462 2.47 - 4.93: 205 4.93 - 7.40: 32 7.40 - 9.87: 12 9.87 - 12.33: 4 Bond angle restraints: 11715 Sorted by residual: angle pdb=" N ALA A 659 " pdb=" CA ALA A 659 " pdb=" C ALA A 659 " ideal model delta sigma weight residual 109.07 119.88 -10.81 1.52e+00 4.33e-01 5.06e+01 angle pdb=" N TRP A 467 " pdb=" CA TRP A 467 " pdb=" C TRP A 467 " ideal model delta sigma weight residual 111.07 103.85 7.22 1.07e+00 8.73e-01 4.56e+01 angle pdb=" C TRP A 467 " pdb=" CA TRP A 467 " pdb=" CB TRP A 467 " ideal model delta sigma weight residual 110.88 102.33 8.55 1.57e+00 4.06e-01 2.97e+01 angle pdb=" CA TRP A 467 " pdb=" CB TRP A 467 " pdb=" CG TRP A 467 " ideal model delta sigma weight residual 113.60 122.81 -9.21 1.90e+00 2.77e-01 2.35e+01 angle pdb=" N ASP A 658 " pdb=" CA ASP A 658 " pdb=" C ASP A 658 " ideal model delta sigma weight residual 111.36 116.26 -4.90 1.09e+00 8.42e-01 2.02e+01 ... (remaining 11710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4458 16.60 - 33.20: 449 33.20 - 49.80: 167 49.80 - 66.40: 20 66.40 - 82.99: 12 Dihedral angle restraints: 5106 sinusoidal: 1928 harmonic: 3178 Sorted by residual: dihedral pdb=" CA ALA A 659 " pdb=" C ALA A 659 " pdb=" N TYR A 660 " pdb=" CA TYR A 660 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" C TRP A 467 " pdb=" N TRP A 467 " pdb=" CA TRP A 467 " pdb=" CB TRP A 467 " ideal model delta harmonic sigma weight residual -122.60 -110.96 -11.64 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" CA HIS A 406 " pdb=" C HIS A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual -180.00 -157.00 -23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 5103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1122 0.061 - 0.121: 219 0.121 - 0.182: 20 0.182 - 0.242: 6 0.242 - 0.303: 2 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA LYS B 409 " pdb=" N LYS B 409 " pdb=" C LYS B 409 " pdb=" CB LYS B 409 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASN B 404 " pdb=" N ASN B 404 " pdb=" C ASN B 404 " pdb=" CB ASN B 404 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA GLU B 405 " pdb=" N GLU B 405 " pdb=" C GLU B 405 " pdb=" CB GLU B 405 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1366 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 657 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C LEU A 657 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU A 657 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 658 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 410 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO B 411 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 574 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO B 575 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 575 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 575 " 0.032 5.00e-02 4.00e+02 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 46 2.54 - 3.13: 6458 3.13 - 3.72: 12923 3.72 - 4.31: 18271 4.31 - 4.90: 31659 Nonbonded interactions: 69357 Sorted by model distance: nonbonded pdb=" O5' G2P A1001 " pdb="MG MG A1002 " model vdw 1.951 2.170 nonbonded pdb=" O3B G2P A1001 " pdb="MG MG A1003 " model vdw 2.050 2.170 nonbonded pdb=" O SER B 249 " pdb=" OG SER B 252 " model vdw 2.206 3.040 nonbonded pdb=" O GLY A 337 " pdb=" OG1 THR A 340 " model vdw 2.209 3.040 nonbonded pdb=" O ILE B 111 " pdb=" NH2 ARG B 360 " model vdw 2.214 3.120 ... (remaining 69352 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=0.00 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: 1.060 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.610 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.011 0.368 8621 Z= 0.467 Angle : 0.845 12.335 11715 Z= 0.431 Chirality : 0.049 0.303 1369 Planarity : 0.005 0.059 1471 Dihedral : 15.708 82.995 3046 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.18 % Favored : 96.63 % Rotamer: Outliers : 0.46 % Allowed : 20.82 % Favored : 78.73 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.17 % 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: -0.23 (0.25), residues: 1069 helix: 0.46 (0.23), residues: 512 sheet: -0.11 (0.35), residues: 222 loop : -0.94 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 570 TYR 0.018 0.002 TYR B 112 PHE 0.018 0.002 PHE B 75 TRP 0.021 0.004 TRP A 467 HIS 0.008 0.001 HIS A 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00976 / 0.47 ( 8620) covalent geometry : angle 0.84478 / 0.43 (11715) hydrogen bonds : bond 0.14907 / 10.21 ( 477) hydrogen bonds : angle 7.02237 / 5.02 ( 1458) Misc. bond : bond 0.36751 / 19.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.323 Fit side-chains REVERT: A 253 LEU cc_start: 0.8330 (mt) cc_final: 0.8077 (mp) outliers start: 4 outliers final: 2 residues processed: 100 average time/residue: 0.0710 time to fit residues: 10.7737 Evaluate side-chains 97 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.0020 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 0.0170 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN A 470 GLN A 600 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133733 restraints weight = 11906.211| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.89 r_work: 0.3401 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.248 8621 Z= 0.122 Angle : 0.566 8.439 11715 Z= 0.296 Chirality : 0.042 0.144 1369 Planarity : 0.004 0.053 1471 Dihedral : 5.581 64.309 1179 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.71 % Allowed : 19.80 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.52 (0.25), residues: 1069 helix: 1.50 (0.23), residues: 505 sheet: -0.24 (0.34), residues: 229 loop : -0.91 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 570 TYR 0.017 0.001 TYR B 479 PHE 0.017 0.001 PHE B 75 TRP 0.010 0.002 TRP B 22 HIS 0.003 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8620) covalent geometry : angle 0.56568 / 0.30 (11715) hydrogen bonds : bond 0.04828 / 3.36 ( 477) hydrogen bonds : angle 4.82308 / 3.48 ( 1458) Misc. bond : bond 0.24775 / 13.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.337 Fit side-chains REVERT: A 83 PHE cc_start: 0.7867 (m-80) cc_final: 0.7656 (m-80) REVERT: A 335 PHE cc_start: 0.7764 (t80) cc_final: 0.7385 (t80) REVERT: A 458 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.6292 (p90) REVERT: B 93 ASN cc_start: 0.7981 (t0) cc_final: 0.7736 (t0) REVERT: B 360 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7758 (tpp-160) REVERT: B 406 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8760 (mp) REVERT: B 570 ARG cc_start: 0.7656 (mtt90) cc_final: 0.7002 (mtt90) outliers start: 15 outliers final: 7 residues processed: 116 average time/residue: 0.0707 time to fit residues: 12.5753 Evaluate side-chains 105 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 541 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN B 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133036 restraints weight = 12253.479| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.91 r_work: 0.3361 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.319 8621 Z= 0.139 Angle : 0.557 8.598 11715 Z= 0.287 Chirality : 0.042 0.149 1369 Planarity : 0.004 0.053 1471 Dihedral : 5.501 65.088 1178 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.28 % Allowed : 20.25 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1069 helix: 1.72 (0.23), residues: 505 sheet: -0.20 (0.33), residues: 229 loop : -0.87 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.015 0.001 TYR B 479 PHE 0.015 0.001 PHE B 75 TRP 0.012 0.002 TRP A 467 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 8620) covalent geometry : angle 0.55687 / 0.29 (11715) hydrogen bonds : bond 0.04563 / 3.17 ( 477) hydrogen bonds : angle 4.54425 / 3.28 ( 1458) Misc. bond : bond 0.31895 / 16.79 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.325 Fit side-chains REVERT: A 258 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7370 (m-70) REVERT: A 335 PHE cc_start: 0.7744 (t80) cc_final: 0.7458 (t80) REVERT: B 93 ASN cc_start: 0.7965 (t0) cc_final: 0.7713 (t0) REVERT: B 360 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7847 (tpp-160) REVERT: B 570 ARG cc_start: 0.7608 (mtt90) cc_final: 0.6937 (mtt90) outliers start: 20 outliers final: 9 residues processed: 113 average time/residue: 0.0746 time to fit residues: 12.7001 Evaluate side-chains 105 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 320 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134624 restraints weight = 12413.121| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.81 r_work: 0.3385 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.349 8621 Z= 0.133 Angle : 0.542 8.663 11715 Z= 0.278 Chirality : 0.042 0.148 1369 Planarity : 0.004 0.051 1471 Dihedral : 5.468 64.599 1178 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.73 % Allowed : 20.36 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.81 (0.26), residues: 1069 helix: 1.81 (0.23), residues: 505 sheet: -0.08 (0.34), residues: 224 loop : -0.94 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.015 0.001 TYR B 479 PHE 0.015 0.001 PHE B 75 TRP 0.012 0.002 TRP A 467 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 8620) covalent geometry : angle 0.54184 / 0.28 (11715) hydrogen bonds : bond 0.04365 / 3.03 ( 477) hydrogen bonds : angle 4.41197 / 3.19 ( 1458) Misc. bond : bond 0.34931 / 18.38 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.319 Fit side-chains REVERT: A 150 ASN cc_start: 0.7175 (OUTLIER) cc_final: 0.6878 (m-40) REVERT: A 258 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7368 (m-70) REVERT: A 335 PHE cc_start: 0.7804 (t80) cc_final: 0.7580 (t80) REVERT: A 473 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7642 (mp-120) REVERT: B 93 ASN cc_start: 0.7887 (t0) cc_final: 0.7652 (t0) REVERT: B 279 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.8256 (ttp80) REVERT: B 360 ARG cc_start: 0.8164 (tpp-160) cc_final: 0.7833 (tpp-160) REVERT: B 570 ARG cc_start: 0.7555 (mtt90) cc_final: 0.6886 (mtt90) REVERT: B 600 GLN cc_start: 0.7936 (mt0) cc_final: 0.7452 (mm-40) outliers start: 24 outliers final: 13 residues processed: 125 average time/residue: 0.0848 time to fit residues: 15.4535 Evaluate side-chains 113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.163528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135462 restraints weight = 12435.910| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.92 r_work: 0.3360 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.387 8621 Z= 0.147 Angle : 0.548 8.804 11715 Z= 0.279 Chirality : 0.042 0.163 1369 Planarity : 0.004 0.050 1471 Dihedral : 5.500 64.801 1178 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.62 % Allowed : 21.27 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.81 (0.26), residues: 1069 helix: 1.82 (0.23), residues: 505 sheet: -0.07 (0.34), residues: 224 loop : -0.94 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.014 0.001 TYR B 479 PHE 0.015 0.001 PHE B 75 TRP 0.014 0.002 TRP A 467 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 8620) covalent geometry : angle 0.54768 / 0.28 (11715) hydrogen bonds : bond 0.04391 / 3.04 ( 477) hydrogen bonds : angle 4.39553 / 3.19 ( 1458) Misc. bond : bond 0.38747 / 20.39 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.331 Fit side-chains REVERT: A 258 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7440 (m-70) REVERT: A 335 PHE cc_start: 0.7792 (t80) cc_final: 0.7496 (t80) REVERT: A 473 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7662 (mp-120) REVERT: B 93 ASN cc_start: 0.7964 (t0) cc_final: 0.7706 (t0) REVERT: B 279 ARG cc_start: 0.8527 (ttt-90) cc_final: 0.8259 (ttp80) REVERT: B 360 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7868 (tpp-160) REVERT: B 570 ARG cc_start: 0.7559 (mtt90) cc_final: 0.6920 (mtt90) REVERT: B 600 GLN cc_start: 0.7937 (mt0) cc_final: 0.7690 (mp10) outliers start: 23 outliers final: 15 residues processed: 121 average time/residue: 0.0818 time to fit residues: 14.4224 Evaluate side-chains 114 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 541 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128320 restraints weight = 12336.014| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.95 r_work: 0.3366 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.402 8621 Z= 0.149 Angle : 0.552 8.885 11715 Z= 0.280 Chirality : 0.042 0.160 1369 Planarity : 0.004 0.050 1471 Dihedral : 5.219 64.991 1176 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.96 % Allowed : 21.73 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.84 (0.26), residues: 1069 helix: 1.84 (0.23), residues: 505 sheet: -0.06 (0.34), residues: 224 loop : -0.92 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 570 TYR 0.014 0.001 TYR B 211 PHE 0.014 0.001 PHE B 75 TRP 0.014 0.002 TRP A 467 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 8620) covalent geometry : angle 0.55155 / 0.28 (11715) hydrogen bonds : bond 0.04375 / 3.03 ( 477) hydrogen bonds : angle 4.36901 / 3.17 ( 1458) Misc. bond : bond 0.40211 / 21.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.490 Fit side-chains REVERT: A 258 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7461 (m-70) REVERT: A 335 PHE cc_start: 0.7718 (t80) cc_final: 0.7333 (t80) REVERT: A 473 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7610 (mp-120) REVERT: B 93 ASN cc_start: 0.7923 (t0) cc_final: 0.7664 (t0) REVERT: B 360 ARG cc_start: 0.8154 (tpp-160) cc_final: 0.7887 (tpp-160) REVERT: B 600 GLN cc_start: 0.7855 (mt0) cc_final: 0.7448 (mm-40) outliers start: 26 outliers final: 17 residues processed: 123 average time/residue: 0.0904 time to fit residues: 15.7098 Evaluate side-chains 111 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 563 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.159815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130269 restraints weight = 16947.880| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.40 r_work: 0.3337 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.365 8621 Z= 0.133 Angle : 0.539 8.815 11715 Z= 0.274 Chirality : 0.042 0.156 1369 Planarity : 0.004 0.049 1471 Dihedral : 5.195 64.142 1176 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.62 % Allowed : 22.53 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.89 (0.26), residues: 1069 helix: 1.89 (0.23), residues: 505 sheet: -0.05 (0.34), residues: 224 loop : -0.91 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 570 TYR 0.014 0.001 TYR B 479 PHE 0.015 0.001 PHE B 75 TRP 0.013 0.002 TRP A 467 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 8620) covalent geometry : angle 0.53853 / 0.27 (11715) hydrogen bonds : bond 0.04241 / 2.94 ( 477) hydrogen bonds : angle 4.31129 / 3.13 ( 1458) Misc. bond : bond 0.36530 / 19.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.323 Fit side-chains REVERT: A 258 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7492 (m-70) REVERT: A 335 PHE cc_start: 0.7711 (t80) cc_final: 0.7319 (t80) REVERT: A 473 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7684 (mp-120) REVERT: A 502 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 93 ASN cc_start: 0.7943 (t0) cc_final: 0.7713 (t0) REVERT: B 360 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7972 (tpp-160) REVERT: B 600 GLN cc_start: 0.7978 (mt0) cc_final: 0.7570 (mm-40) outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 0.0821 time to fit residues: 13.7865 Evaluate side-chains 115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.163985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132904 restraints weight = 10159.840| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.91 r_work: 0.3384 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.329 8621 Z= 0.124 Angle : 0.543 8.762 11715 Z= 0.277 Chirality : 0.041 0.152 1369 Planarity : 0.004 0.049 1471 Dihedral : 5.169 63.765 1176 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.62 % Allowed : 22.30 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.95 (0.26), residues: 1069 helix: 1.95 (0.23), residues: 505 sheet: -0.05 (0.34), residues: 224 loop : -0.88 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 570 TYR 0.013 0.001 TYR B 211 PHE 0.014 0.001 PHE B 75 TRP 0.013 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 8620) covalent geometry : angle 0.54261 / 0.28 (11715) hydrogen bonds : bond 0.04152 / 2.88 ( 477) hydrogen bonds : angle 4.28359 / 3.10 ( 1458) Misc. bond : bond 0.32853 / 17.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.322 Fit side-chains REVERT: A 258 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7492 (m-70) REVERT: A 335 PHE cc_start: 0.7695 (t80) cc_final: 0.7228 (t80) REVERT: A 502 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 93 ASN cc_start: 0.7851 (t0) cc_final: 0.7615 (t0) REVERT: B 360 ARG cc_start: 0.8119 (tpp-160) cc_final: 0.7917 (tpp-160) REVERT: B 600 GLN cc_start: 0.7939 (mt0) cc_final: 0.7587 (mm-40) outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 0.0808 time to fit residues: 13.5419 Evaluate side-chains 113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 541 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 97 optimal weight: 0.0270 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 563 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134899 restraints weight = 11898.859| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.21 r_work: 0.3426 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.206 8621 Z= 0.102 Angle : 0.517 8.556 11715 Z= 0.263 Chirality : 0.041 0.158 1369 Planarity : 0.004 0.049 1471 Dihedral : 5.058 63.178 1176 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.39 % Allowed : 22.30 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.07 (0.26), residues: 1069 helix: 2.09 (0.23), residues: 508 sheet: -0.04 (0.34), residues: 234 loop : -0.92 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 570 TYR 0.014 0.001 TYR B 211 PHE 0.015 0.001 PHE B 223 TRP 0.009 0.001 TRP A 467 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 8620) covalent geometry : angle 0.51732 / 0.26 (11715) hydrogen bonds : bond 0.03825 / 2.66 ( 477) hydrogen bonds : angle 4.15481 / 3.01 ( 1458) Misc. bond : bond 0.20648 / 10.87 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.342 Fit side-chains REVERT: A 220 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8013 (ttpp) REVERT: A 258 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7575 (m-70) REVERT: A 335 PHE cc_start: 0.7711 (t80) cc_final: 0.7271 (t80) REVERT: A 458 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7438 (p90) outliers start: 21 outliers final: 14 residues processed: 126 average time/residue: 0.0806 time to fit residues: 14.8997 Evaluate side-chains 115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 46 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 11 optimal weight: 0.0000 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN B 266 HIS B 600 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.163755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134458 restraints weight = 10051.633| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.69 r_work: 0.3435 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 8621 Z= 0.114 Angle : 0.545 10.999 11715 Z= 0.272 Chirality : 0.041 0.158 1369 Planarity : 0.004 0.049 1471 Dihedral : 5.047 62.279 1176 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.93 % Allowed : 23.55 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.13 (0.26), residues: 1069 helix: 2.13 (0.23), residues: 509 sheet: 0.05 (0.34), residues: 229 loop : -0.90 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 570 TYR 0.023 0.001 TYR A 372 PHE 0.014 0.001 PHE B 75 TRP 0.010 0.002 TRP B 602 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 8620) covalent geometry : angle 0.54454 / 0.27 (11715) hydrogen bonds : bond 0.03897 / 2.71 ( 477) hydrogen bonds : angle 4.13452 / 3.00 ( 1458) Misc. bond : bond 0.22779 / 11.99 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.299 Fit side-chains REVERT: A 220 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7967 (ttpp) REVERT: A 258 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7558 (m-70) REVERT: A 335 PHE cc_start: 0.7643 (t80) cc_final: 0.7315 (t80) REVERT: B 73 MET cc_start: 0.8231 (tpp) cc_final: 0.7937 (tpp) outliers start: 17 outliers final: 14 residues processed: 116 average time/residue: 0.0764 time to fit residues: 13.0889 Evaluate side-chains 117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.163944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131704 restraints weight = 17060.179| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.60 r_work: 0.3324 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.305 8621 Z= 0.142 Angle : 0.563 10.055 11715 Z= 0.283 Chirality : 0.042 0.152 1369 Planarity : 0.004 0.050 1471 Dihedral : 5.112 62.373 1176 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.28 % Allowed : 22.87 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.08 (0.26), residues: 1069 helix: 2.06 (0.23), residues: 508 sheet: 0.00 (0.33), residues: 229 loop : -0.84 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 570 TYR 0.032 0.001 TYR A 372 PHE 0.014 0.001 PHE B 75 TRP 0.014 0.002 TRP A 467 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 8620) covalent geometry : angle 0.56327 / 0.28 (11715) hydrogen bonds : bond 0.04125 / 2.86 ( 477) hydrogen bonds : angle 4.20987 / 3.06 ( 1458) Misc. bond : bond 0.30470 / 16.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2661.57 seconds wall clock time: 46 minutes 24.25 seconds (2784.25 seconds total)