Starting phenix.real_space_refine on Fri Nov 15 12:40:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/11_2024/8hbf_34627.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/11_2024/8hbf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/11_2024/8hbf_34627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/11_2024/8hbf_34627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/11_2024/8hbf_34627.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/11_2024/8hbf_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.58, per 1000 atoms: 0.90 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 1.5 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: 1.06 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: 2.93 Time building geometry restraints manager: 2.56 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: 0.680 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.730 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- 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 : 1.087 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: 0.1724 time to fit residues: 25.7537 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 : 0.950 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.6980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0743 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= 0.228 Angle : 0.582 8.401 11715 Z= 0.305 Chirality : 0.043 0.149 1369 Planarity : 0.004 0.054 1471 Dihedral : 6.759 79.558 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 : 1.016 Fit side-chains REVERT: A 335 PHE cc_start: 0.7834 (t80) cc_final: 0.7476 (t80) REVERT: A 370 MET cc_start: 0.8065 (mtt) cc_final: 0.7862 (mtt) REVERT: A 443 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8139 (mp) REVERT: B 93 ASN cc_start: 0.7942 (t0) cc_final: 0.7585 (t0) REVERT: B 360 ARG cc_start: 0.8202 (tpp-160) cc_final: 0.7722 (tpp-160) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.1666 time to fit residues: 28.8231 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 : 0.923 ------------------------------------------------------------------------------- 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 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 0.0050 chunk 107 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1167 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= 0.186 Angle : 0.547 12.470 11715 Z= 0.280 Chirality : 0.042 0.149 1369 Planarity : 0.004 0.053 1471 Dihedral : 6.509 75.634 1206 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.62 % Allowed : 19.34 % Favored : 78.04 % 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: 0.76 (0.26), residues: 1069 helix: 1.76 (0.23), residues: 506 sheet: -0.21 (0.33), residues: 229 loop : -0.85 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 467 HIS 0.003 0.001 HIS B 492 PHE 0.016 0.001 PHE B 75 TYR 0.015 0.001 TYR B 479 ARG 0.002 0.000 ARG B 350 *********************** 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 125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.974 Fit side-chains REVERT: A 258 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7301 (m-70) REVERT: A 335 PHE cc_start: 0.7831 (t80) cc_final: 0.7580 (t80) REVERT: A 473 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7576 (mp-120) REVERT: B 93 ASN cc_start: 0.7848 (t0) cc_final: 0.7527 (t0) REVERT: B 279 ARG cc_start: 0.8217 (ttt-90) cc_final: 0.7940 (ttp80) REVERT: B 360 ARG cc_start: 0.8120 (tpp-160) cc_final: 0.7782 (tpp-160) outliers start: 23 outliers final: 12 residues processed: 121 average time/residue: 0.1690 time to fit residues: 30.4619 Evaluate side-chains 110 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0770 chunk 74 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.0770 chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1454 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= 0.159 Angle : 0.524 9.444 11715 Z= 0.265 Chirality : 0.041 0.147 1369 Planarity : 0.004 0.052 1471 Dihedral : 6.370 71.939 1206 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.39 % Allowed : 20.82 % Favored : 76.79 % 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: 0.91 (0.26), residues: 1069 helix: 1.93 (0.23), residues: 506 sheet: -0.06 (0.34), residues: 224 loop : -0.93 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 PHE 0.015 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 ARG 0.005 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 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.992 Fit side-chains REVERT: A 258 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7385 (m-70) REVERT: A 335 PHE cc_start: 0.7744 (t80) cc_final: 0.7495 (t80) REVERT: A 458 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7088 (p90) REVERT: B 73 MET cc_start: 0.8353 (tpp) cc_final: 0.8144 (tpp) REVERT: B 279 ARG cc_start: 0.8176 (ttt-90) cc_final: 0.7939 (ttp80) REVERT: B 360 ARG cc_start: 0.8083 (tpp-160) cc_final: 0.7790 (tpp-160) REVERT: B 600 GLN cc_start: 0.7600 (mt0) cc_final: 0.7273 (mm-40) outliers start: 21 outliers final: 13 residues processed: 127 average time/residue: 0.2004 time to fit residues: 36.0997 Evaluate side-chains 115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 483 LEU 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 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 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 0.0000 chunk 43 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1575 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= 0.180 Angle : 0.535 9.545 11715 Z= 0.268 Chirality : 0.041 0.163 1369 Planarity : 0.004 0.051 1471 Dihedral : 6.324 69.178 1206 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.62 % Allowed : 21.73 % 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: 0.99 (0.26), residues: 1069 helix: 2.02 (0.23), residues: 507 sheet: -0.06 (0.34), residues: 224 loop : -0.91 (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 105 PHE 0.014 0.001 PHE B 75 TYR 0.015 0.001 TYR B 479 ARG 0.005 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 123 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.971 Fit side-chains REVERT: A 258 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7401 (m-70) REVERT: A 335 PHE cc_start: 0.7757 (t80) cc_final: 0.7372 (t80) REVERT: B 279 ARG cc_start: 0.8175 (ttt-90) cc_final: 0.7932 (ttp80) REVERT: B 360 ARG cc_start: 0.8059 (tpp-160) cc_final: 0.7790 (tpp-160) REVERT: B 600 GLN cc_start: 0.7632 (mt0) cc_final: 0.7342 (mm-40) outliers start: 23 outliers final: 15 residues processed: 118 average time/residue: 0.1871 time to fit residues: 31.7876 Evaluate side-chains 112 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0980 chunk 20 optimal weight: 0.0010 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1667 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= 0.168 Angle : 0.525 9.134 11715 Z= 0.263 Chirality : 0.041 0.161 1369 Planarity : 0.004 0.050 1471 Dihedral : 6.022 67.321 1204 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.28 % Allowed : 22.07 % 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: 1.06 (0.26), residues: 1069 helix: 2.10 (0.23), residues: 507 sheet: 0.02 (0.34), residues: 219 loop : -0.93 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.003 0.001 HIS A 545 PHE 0.014 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 ARG 0.007 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 120 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.871 Fit side-chains REVERT: A 258 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7422 (m-70) REVERT: A 335 PHE cc_start: 0.7772 (t80) cc_final: 0.7323 (t80) REVERT: A 341 MET cc_start: 0.6313 (mmm) cc_final: 0.5948 (mmm) REVERT: B 73 MET cc_start: 0.8383 (tpp) cc_final: 0.8092 (tpp) REVERT: B 279 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7930 (ttp80) outliers start: 20 outliers final: 15 residues processed: 116 average time/residue: 0.1828 time to fit residues: 30.8480 Evaluate side-chains 109 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 443 LEU 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 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 ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 0.0010 chunk 58 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1679 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= 0.192 Angle : 0.539 9.073 11715 Z= 0.273 Chirality : 0.041 0.149 1369 Planarity : 0.004 0.049 1471 Dihedral : 6.011 64.834 1204 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.62 % Allowed : 22.07 % 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 (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: 1.13 (0.26), residues: 1069 helix: 2.13 (0.23), residues: 507 sheet: 0.07 (0.34), residues: 219 loop : -0.87 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 467 HIS 0.004 0.001 HIS B 266 PHE 0.014 0.001 PHE B 75 TYR 0.015 0.001 TYR B 211 ARG 0.005 0.000 ARG B 570 *********************** 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 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.959 Fit side-chains REVERT: A 258 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7435 (m-70) REVERT: A 335 PHE cc_start: 0.7789 (t80) cc_final: 0.7271 (t80) REVERT: A 341 MET cc_start: 0.6434 (mmm) cc_final: 0.6066 (mmm) REVERT: A 364 MET cc_start: 0.7896 (ttp) cc_final: 0.7631 (ptm) REVERT: A 444 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6987 (mm-30) REVERT: A 590 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7760 (ttmm) REVERT: B 73 MET cc_start: 0.8423 (tpp) cc_final: 0.8113 (tpp) REVERT: B 279 ARG cc_start: 0.8149 (ttt-90) cc_final: 0.7921 (ttp80) outliers start: 23 outliers final: 14 residues processed: 117 average time/residue: 0.1854 time to fit residues: 31.1407 Evaluate side-chains 110 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 A residue 590 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 20 optimal weight: 0.0970 chunk 66 optimal weight: 0.5980 chunk 71 optimal weight: 0.0020 chunk 51 optimal weight: 0.0770 chunk 9 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1869 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= 0.143 Angle : 0.519 9.023 11715 Z= 0.260 Chirality : 0.041 0.144 1369 Planarity : 0.004 0.049 1471 Dihedral : 5.906 65.085 1204 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.93 % Allowed : 22.98 % 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 (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: 1.25 (0.26), residues: 1069 helix: 2.27 (0.23), residues: 512 sheet: 0.10 (0.34), residues: 229 loop : -0.95 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 22 HIS 0.004 0.001 HIS B 266 PHE 0.014 0.001 PHE B 75 TYR 0.013 0.001 TYR B 211 ARG 0.005 0.000 ARG B 570 *********************** 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 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.016 Fit side-chains REVERT: A 220 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8066 (ttpp) REVERT: A 258 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7469 (m-70) REVERT: A 335 PHE cc_start: 0.7736 (t80) cc_final: 0.7195 (t80) REVERT: A 364 MET cc_start: 0.7916 (ttp) cc_final: 0.7672 (ptm) REVERT: A 444 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 458 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7421 (p90) REVERT: B 9 LEU cc_start: 0.8206 (tp) cc_final: 0.8003 (mt) REVERT: B 73 MET cc_start: 0.8395 (tpp) cc_final: 0.8150 (tpp) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.1978 time to fit residues: 34.9145 Evaluate side-chains 113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 547 VAL 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 420 VAL 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 97 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 88 optimal weight: 0.0070 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8620 Z= 0.172 Angle : 0.538 9.948 11715 Z= 0.266 Chirality : 0.041 0.145 1369 Planarity : 0.004 0.049 1471 Dihedral : 5.905 63.017 1204 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.16 % Allowed : 22.53 % 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 (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: 1.27 (0.26), residues: 1069 helix: 2.25 (0.23), residues: 510 sheet: 0.12 (0.34), residues: 229 loop : -0.86 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 467 HIS 0.005 0.001 HIS B 266 PHE 0.013 0.001 PHE B 223 TYR 0.013 0.001 TYR B 211 ARG 0.006 0.000 ARG B 279 *********************** 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 121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.889 Fit side-chains REVERT: A 220 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8079 (ttpp) REVERT: A 258 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7567 (m-70) REVERT: A 335 PHE cc_start: 0.7776 (t80) cc_final: 0.7293 (t80) REVERT: A 364 MET cc_start: 0.7990 (ttp) cc_final: 0.7730 (ptm) REVERT: A 590 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7613 (ttmm) REVERT: B 9 LEU cc_start: 0.8241 (tp) cc_final: 0.8031 (mt) REVERT: B 73 MET cc_start: 0.8430 (tpp) cc_final: 0.8144 (tpp) outliers start: 19 outliers final: 13 residues processed: 118 average time/residue: 0.1983 time to fit residues: 33.8363 Evaluate side-chains 115 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 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 A residue 590 LYS 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 474 THR Chi-restraints excluded: chain B residue 541 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0070 chunk 71 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1871 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= 0.180 Angle : 0.544 9.639 11715 Z= 0.268 Chirality : 0.041 0.147 1369 Planarity : 0.004 0.050 1471 Dihedral : 5.912 61.698 1204 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.71 % Allowed : 22.64 % 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: 1.28 (0.26), residues: 1069 helix: 2.26 (0.23), residues: 509 sheet: 0.11 (0.33), residues: 229 loop : -0.84 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 602 HIS 0.005 0.001 HIS B 266 PHE 0.013 0.001 PHE B 223 TYR 0.012 0.001 TYR B 479 ARG 0.007 0.000 ARG B 279 ********************** 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 117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.955 Fit side-chains REVERT: A 220 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7997 (ttpp) REVERT: A 258 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7588 (m-70) REVERT: A 335 PHE cc_start: 0.7753 (t80) cc_final: 0.7241 (t80) REVERT: A 364 MET cc_start: 0.7943 (ttp) cc_final: 0.7710 (ptm) REVERT: B 9 LEU cc_start: 0.8246 (tp) cc_final: 0.8032 (mt) REVERT: B 73 MET cc_start: 0.8434 (tpp) cc_final: 0.8144 (tpp) REVERT: B 570 ARG cc_start: 0.7320 (mtt90) cc_final: 0.6614 (mtt90) outliers start: 15 outliers final: 14 residues processed: 114 average time/residue: 0.2005 time to fit residues: 33.3172 Evaluate side-chains 116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 429 LEU 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 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 541 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 88 optimal weight: 0.0970 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.162268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134023 restraints weight = 12229.929| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.87 r_work: 0.3396 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 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 = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1821 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= 0.208 Angle : 0.555 9.437 11715 Z= 0.275 Chirality : 0.041 0.149 1369 Planarity : 0.004 0.049 1471 Dihedral : 5.962 61.560 1204 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.05 % Allowed : 22.41 % Favored : 75.54 % 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: 1.24 (0.26), residues: 1069 helix: 2.21 (0.23), residues: 509 sheet: 0.09 (0.33), residues: 229 loop : -0.82 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 602 HIS 0.005 0.001 HIS B 266 PHE 0.013 0.001 PHE B 75 TYR 0.013 0.001 TYR B 479 ARG 0.007 0.000 ARG B 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.45 seconds wall clock time: 37 minutes 56.34 seconds (2276.34 seconds total)