Starting phenix.real_space_refine on Thu Mar 13 12:56:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbf_34627/03_2025/8hbf_34627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbf_34627/03_2025/8hbf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hbf_34627/03_2025/8hbf_34627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbf_34627/03_2025/8hbf_34627.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbf_34627/03_2025/8hbf_34627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbf_34627/03_2025/8hbf_34627.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'GLU:plan': 18, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 18, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} 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: 7.54, per 1000 atoms: 0.89 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: 2.29 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.99 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: 2.90 Time building geometry restraints manager: 2.51 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 - 17.19: 4494 17.19 - 34.38: 458 34.38 - 51.57: 154 51.57 - 68.75: 15 68.75 - 85.94: 13 Dihedral angle restraints: 5134 sinusoidal: 1956 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 5131 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: 1.280 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.960 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 0.219 8620 Z= 0.625 Angle : 0.845 12.335 11715 Z= 0.431 Chirality : 0.049 0.303 1369 Planarity : 0.005 0.059 1471 Dihedral : 15.942 85.944 3074 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.021 0.004 TRP A 467 HIS 0.008 0.001 HIS A 578 PHE 0.018 0.002 PHE B 75 TYR 0.018 0.002 TYR B 112 ARG 0.005 0.000 ARG B 570 *********************** 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 : 0.882 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: 0.1665 time to fit residues: 25.1079 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 : 0.855 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3870 r_free = 0.3870 target = 0.161665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130708 restraints weight = 11824.838| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.99 r_work: 0.3361 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 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 = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8620 Z= 0.227 Angle : 0.582 8.404 11715 Z= 0.305 Chirality : 0.043 0.150 1369 Planarity : 0.004 0.054 1471 Dihedral : 6.762 79.619 1207 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.05 % Allowed : 19.80 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1069 helix: 1.38 (0.23), residues: 505 sheet: -0.24 (0.34), residues: 229 loop : -0.93 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 467 HIS 0.004 0.001 HIS B 492 PHE 0.017 0.002 PHE B 75 TYR 0.016 0.001 TYR B 479 ARG 0.004 0.000 ARG B 570 *********************** 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: 18 poor density : 101 time to evaluate : 0.924 Fit side-chains REVERT: A 335 PHE cc_start: 0.7794 (t80) cc_final: 0.7377 (t80) REVERT: A 370 MET cc_start: 0.8205 (mtt) cc_final: 0.7992 (mtt) REVERT: A 443 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7942 (mp) REVERT: B 93 ASN cc_start: 0.8043 (t0) cc_final: 0.7768 (t0) REVERT: B 360 ARG cc_start: 0.8254 (tpp-160) cc_final: 0.7782 (tpp-160) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.1664 time to fit residues: 28.7784 Evaluate side-chains 107 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 PHE 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 443 LEU 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 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 607 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 0.0070 chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 95 optimal weight: 0.0470 chunk 12 optimal weight: 5.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3931 r_free = 0.3931 target = 0.167595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139458 restraints weight = 12012.437| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.98 r_work: 0.3402 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 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 = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8620 Z= 0.158 Angle : 0.533 12.210 11715 Z= 0.273 Chirality : 0.041 0.147 1369 Planarity : 0.004 0.053 1471 Dihedral : 6.458 76.687 1206 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.05 % Allowed : 20.02 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1069 helix: 1.84 (0.23), residues: 506 sheet: -0.20 (0.33), residues: 229 loop : -0.85 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 PHE 0.017 0.001 PHE B 223 TYR 0.015 0.001 TYR B 479 ARG 0.004 0.000 ARG B 225 *********************** 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 121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.884 Fit side-chains REVERT: A 258 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7366 (m-70) REVERT: A 335 PHE cc_start: 0.7729 (t80) cc_final: 0.7432 (t80) REVERT: A 458 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7197 (p90) REVERT: B 279 ARG cc_start: 0.8565 (ttt-90) cc_final: 0.8299 (ttp80) REVERT: B 570 ARG cc_start: 0.7612 (mtt90) cc_final: 0.6863 (mtt90) REVERT: B 600 GLN cc_start: 0.7972 (mt0) cc_final: 0.7457 (mm-40) outliers start: 18 outliers final: 6 residues processed: 116 average time/residue: 0.1794 time to fit residues: 30.5016 Evaluate side-chains 104 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 458 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 541 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 11 optimal weight: 0.0030 chunk 38 optimal weight: 0.7980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3931 r_free = 0.3931 target = 0.167811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139039 restraints weight = 12336.897| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.13 r_work: 0.3406 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 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 = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8620 Z= 0.158 Angle : 0.523 9.395 11715 Z= 0.265 Chirality : 0.041 0.149 1369 Planarity : 0.004 0.052 1471 Dihedral : 6.335 72.610 1206 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.71 % Allowed : 21.73 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1069 helix: 1.99 (0.23), residues: 507 sheet: -0.05 (0.34), residues: 224 loop : -0.90 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 PHE 0.015 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 ARG 0.002 0.000 ARG B 570 *********************** 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 124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.861 Fit side-chains REVERT: A 150 ASN cc_start: 0.7117 (OUTLIER) cc_final: 0.6791 (m-40) REVERT: A 258 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7459 (m-70) REVERT: A 335 PHE cc_start: 0.7655 (t80) cc_final: 0.7206 (t80) REVERT: A 444 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6336 (mm-30) REVERT: B 279 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.8289 (ttp80) REVERT: B 360 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7882 (tpp-160) REVERT: B 600 GLN cc_start: 0.7939 (mt0) cc_final: 0.7430 (mm-40) outliers start: 15 outliers final: 9 residues processed: 120 average time/residue: 0.1912 time to fit residues: 32.9059 Evaluate side-chains 111 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 301 PHE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135489 restraints weight = 16790.474| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.27 r_work: 0.3383 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8620 Z= 0.195 Angle : 0.533 9.394 11715 Z= 0.269 Chirality : 0.042 0.163 1369 Planarity : 0.004 0.051 1471 Dihedral : 6.339 70.335 1206 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.16 % Allowed : 21.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1069 helix: 1.99 (0.23), residues: 507 sheet: -0.02 (0.34), residues: 224 loop : -0.89 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 467 HIS 0.003 0.001 HIS B 492 PHE 0.014 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 ARG 0.004 0.000 ARG B 570 *********************** 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 117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.857 Fit side-chains REVERT: A 258 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7474 (m-70) REVERT: A 335 PHE cc_start: 0.7638 (t80) cc_final: 0.7196 (t80) REVERT: A 444 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6098 (mm-30) REVERT: B 279 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.8205 (ttp80) REVERT: B 360 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7682 (tpp-160) REVERT: B 600 GLN cc_start: 0.7879 (mt0) cc_final: 0.7527 (mm-40) outliers start: 19 outliers final: 12 residues processed: 112 average time/residue: 0.2436 time to fit residues: 40.6374 Evaluate side-chains 109 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 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 80 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 99 optimal weight: 0.0470 chunk 14 optimal weight: 9.9990 chunk 88 optimal weight: 0.0980 chunk 108 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.167049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136387 restraints weight = 10026.366| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.87 r_work: 0.3424 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 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 = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8620 Z= 0.176 Angle : 0.531 9.068 11715 Z= 0.265 Chirality : 0.041 0.162 1369 Planarity : 0.004 0.051 1471 Dihedral : 6.050 68.041 1204 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.73 % Allowed : 21.62 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1069 helix: 2.05 (0.23), residues: 507 sheet: -0.00 (0.34), residues: 224 loop : -0.89 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 467 HIS 0.003 0.001 HIS B 105 PHE 0.014 0.001 PHE B 75 TYR 0.015 0.001 TYR B 211 ARG 0.004 0.000 ARG B 570 *********************** 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 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.885 Fit side-chains REVERT: A 258 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.7504 (m-70) REVERT: A 335 PHE cc_start: 0.7653 (t80) cc_final: 0.7082 (t80) REVERT: A 444 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6470 (mm-30) REVERT: B 279 ARG cc_start: 0.8491 (ttt-90) cc_final: 0.8234 (ttp80) REVERT: B 360 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7860 (tpp-160) REVERT: B 600 GLN cc_start: 0.7954 (mt0) cc_final: 0.7532 (mm-40) outliers start: 24 outliers final: 16 residues processed: 123 average time/residue: 0.2647 time to fit residues: 46.8699 Evaluate side-chains 113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.3863 > 50: distance: 8 - 195: 4.612 distance: 11 - 192: 5.279 distance: 20 - 183: 6.214 distance: 23 - 180: 6.025 distance: 42 - 162: 4.933 distance: 103 - 187: 3.113 distance: 131 - 132: 4.355 distance: 131 - 134: 3.486 distance: 132 - 133: 8.325 distance: 132 - 137: 7.251 distance: 134 - 135: 3.643 distance: 134 - 136: 4.303 distance: 137 - 138: 5.616 distance: 138 - 139: 10.200 distance: 138 - 141: 5.350 distance: 139 - 140: 14.541 distance: 139 - 145: 14.114 distance: 141 - 142: 4.842 distance: 141 - 143: 5.978 distance: 142 - 144: 5.667 distance: 145 - 146: 11.842 distance: 146 - 147: 36.359 distance: 147 - 148: 25.403 distance: 147 - 149: 17.376 distance: 149 - 150: 13.918 distance: 150 - 151: 12.672 distance: 150 - 153: 18.972 distance: 151 - 152: 5.920 distance: 151 - 157: 4.309 distance: 153 - 154: 19.151 distance: 154 - 155: 9.321 distance: 154 - 156: 4.009 distance: 157 - 158: 5.877 distance: 158 - 159: 6.583 distance: 158 - 161: 10.812 distance: 159 - 160: 12.797 distance: 159 - 162: 7.089 distance: 163 - 166: 3.801 distance: 164 - 165: 3.623 distance: 164 - 174: 5.490 distance: 166 - 167: 3.483 distance: 167 - 168: 3.511 distance: 167 - 169: 5.530 distance: 168 - 170: 4.965 distance: 170 - 172: 5.967 distance: 171 - 172: 9.682 distance: 172 - 173: 3.703 distance: 174 - 175: 3.320 distance: 175 - 176: 3.146 distance: 176 - 177: 3.260 distance: 176 - 180: 3.402 distance: 178 - 179: 6.892 distance: 181 - 182: 3.197 distance: 181 - 184: 4.602 distance: 182 - 183: 5.980 distance: 182 - 187: 4.136 distance: 184 - 185: 4.860 distance: 184 - 186: 10.059 distance: 187 - 188: 3.442 distance: 188 - 189: 5.444 distance: 188 - 191: 3.967 distance: 192 - 193: 5.199 distance: 193 - 194: 3.560 distance: 194 - 195: 5.611 distance: 194 - 196: 6.585