Starting phenix.real_space_refine on Sun Dec 29 01:32:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oj8_12939/12_2024/7oj8_12939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oj8_12939/12_2024/7oj8_12939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oj8_12939/12_2024/7oj8_12939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oj8_12939/12_2024/7oj8_12939.map" model { file = "/net/cci-nas-00/data/ceres_data/7oj8_12939/12_2024/7oj8_12939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oj8_12939/12_2024/7oj8_12939.cif" } resolution = 3.4 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= 0.057 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 59 5.16 5 C 5958 2.51 5 N 1484 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9148 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4475 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 20, 'TRANS': 554} Chain breaks: 3 Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4475 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 20, 'TRANS': 554} Chain breaks: 3 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'ATP': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {'ATP': 1, 'CLR': 2, 'FY5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.55, per 1000 atoms: 0.72 Number of scatterers: 9148 At special positions: 0 Unit cell: (78.66, 90.896, 129.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 6 15.00 O 1641 8.00 N 1484 7.00 C 5958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 61.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.789A pdb=" N LEU A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.506A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.756A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.607A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 4.059A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 4.212A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.730A pdb=" N LYS A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.661A pdb=" N SER A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 391 through 413 removed outlier: 3.844A pdb=" N SER A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 479 through 497 Proline residue: A 485 - end of helix removed outlier: 4.785A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.577A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 551 removed outlier: 3.644A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 removed outlier: 3.529A pdb=" N SER A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TRP A 567 " --> pdb=" O TRP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.560A pdb=" N ASN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.718A pdb=" N THR A 598 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.655A pdb=" N TYR A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 650 Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.790A pdb=" N LEU B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.506A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.757A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 232 removed outlier: 3.608A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 4.059A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 280 removed outlier: 4.214A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.730A pdb=" N LYS B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.661A pdb=" N SER B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 391 through 413 removed outlier: 3.844A pdb=" N SER B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 479 through 497 Proline residue: B 485 - end of helix removed outlier: 4.785A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 528 removed outlier: 3.577A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 551 removed outlier: 3.644A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 571 removed outlier: 3.528A pdb=" N SER B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TRP B 567 " --> pdb=" O TRP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.560A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 598 removed outlier: 3.718A pdb=" N THR B 598 " --> pdb=" O LEU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.656A pdb=" N TYR B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.997A pdb=" N HIS A 40 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 78 removed outlier: 3.523A pdb=" N ILE A 238 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 240 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 255 through 259 removed outlier: 6.587A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.997A pdb=" N HIS B 40 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 78 removed outlier: 3.522A pdb=" N ILE B 238 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 240 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 259 removed outlier: 6.587A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1440 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: 2.62 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1413 1.31 - 1.44: 2494 1.44 - 1.57: 5327 1.57 - 1.70: 27 1.70 - 1.83: 94 Bond restraints: 9355 Sorted by residual: bond pdb=" C5 ATP B1501 " pdb=" N7 ATP B1501 " ideal model delta sigma weight residual 1.387 1.521 -0.134 1.00e-02 1.00e+04 1.79e+02 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.520 -0.133 1.00e-02 1.00e+04 1.76e+02 bond pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.374 1.265 0.109 1.00e-02 1.00e+04 1.18e+02 bond pdb=" C4 ATP B1501 " pdb=" N9 ATP B1501 " ideal model delta sigma weight residual 1.374 1.266 0.108 1.00e-02 1.00e+04 1.16e+02 bond pdb=" C6 ATP A1501 " pdb=" N6 ATP A1501 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.10e+02 ... (remaining 9350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 12598 4.66 - 9.32: 78 9.32 - 13.98: 18 13.98 - 18.63: 7 18.63 - 23.29: 2 Bond angle restraints: 12703 Sorted by residual: angle pdb=" PB ATP B1501 " pdb=" O3B ATP B1501 " pdb=" PG ATP B1501 " ideal model delta sigma weight residual 139.87 116.58 23.29 1.00e+00 1.00e+00 5.43e+02 angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.42e+02 angle pdb=" PA ATP B1501 " pdb=" O3A ATP B1501 " pdb=" PB ATP B1501 " ideal model delta sigma weight residual 136.83 118.24 18.59 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 118.28 18.55 1.00e+00 1.00e+00 3.44e+02 angle pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " pdb=" C8 ATP A1501 " ideal model delta sigma weight residual 105.72 121.87 -16.15 1.00e+00 1.00e+00 2.61e+02 ... (remaining 12698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5340 17.88 - 35.77: 361 35.77 - 53.65: 69 53.65 - 71.53: 12 71.53 - 89.42: 14 Dihedral angle restraints: 5796 sinusoidal: 2482 harmonic: 3314 Sorted by residual: dihedral pdb=" CB CYS B 592 " pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual -86.00 -139.87 53.87 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual -86.00 -139.85 53.85 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA LEU A 64 " pdb=" C LEU A 64 " pdb=" N SER A 65 " pdb=" CA SER A 65 " ideal model delta harmonic sigma weight residual 180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 5793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1253 0.073 - 0.147: 187 0.147 - 0.220: 24 0.220 - 0.294: 10 0.294 - 0.367: 4 Chirality restraints: 1478 Sorted by residual: chirality pdb=" C17 CLR B1503 " pdb=" C13 CLR B1503 " pdb=" C16 CLR B1503 " pdb=" C20 CLR B1503 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C17 CLR A1503 " pdb=" C13 CLR A1503 " pdb=" C16 CLR A1503 " pdb=" C20 CLR A1503 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C17 CLR B1504 " pdb=" C13 CLR B1504 " pdb=" C16 CLR B1504 " pdb=" C20 CLR B1504 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1475 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 65 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C SER B 65 " 0.033 2.00e-02 2.50e+03 pdb=" O SER B 65 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 66 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 65 " 0.010 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C SER A 65 " -0.033 2.00e-02 2.50e+03 pdb=" O SER A 65 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A 66 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 98 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 99 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.026 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 153 2.67 - 3.23: 9428 3.23 - 3.79: 13773 3.79 - 4.34: 18285 4.34 - 4.90: 30462 Nonbonded interactions: 72101 Sorted by model distance: nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.114 3.040 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR A 123 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP B 91 " pdb=" OH TYR B 123 " model vdw 2.249 3.040 nonbonded pdb=" OE1 GLN A 393 " pdb=" OG SER B 535 " model vdw 2.395 3.040 ... (remaining 72096 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 654 or resid 1501 or resid 1503)) selection = (chain 'B' and (resid 34 through 654 or resid 1501 or resid 1503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.110 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 0.190 9355 Z= 0.670 Angle : 1.145 23.292 12703 Z= 0.731 Chirality : 0.059 0.367 1478 Planarity : 0.004 0.046 1544 Dihedral : 13.090 89.418 3659 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.29 % Favored : 94.18 % Rotamer: Outliers : 0.41 % Allowed : 4.38 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.24), residues: 1134 helix: 0.23 (0.19), residues: 672 sheet: -1.55 (0.49), residues: 98 loop : -2.24 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 624 HIS 0.004 0.001 HIS A 283 PHE 0.017 0.002 PHE B 507 TYR 0.016 0.002 TYR B 342 ARG 0.004 0.001 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 261 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8462 (mttt) cc_final: 0.8236 (mttp) REVERT: A 263 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7325 (mmt90) REVERT: A 265 MET cc_start: 0.7120 (mmt) cc_final: 0.6722 (mmp) REVERT: A 521 SER cc_start: 0.9032 (m) cc_final: 0.8795 (p) REVERT: A 523 MET cc_start: 0.8433 (ttp) cc_final: 0.7930 (ttt) REVERT: B 483 MET cc_start: 0.8109 (tmm) cc_final: 0.7846 (ttm) REVERT: B 514 MET cc_start: 0.8531 (mtt) cc_final: 0.8330 (mtm) outliers start: 4 outliers final: 0 residues processed: 265 average time/residue: 0.2403 time to fit residues: 85.2746 Evaluate side-chains 144 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 243 HIS A 283 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 166 GLN B 222 ASN B 299 ASN B 338 ASN B 376 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9355 Z= 0.243 Angle : 0.657 14.947 12703 Z= 0.340 Chirality : 0.045 0.368 1478 Planarity : 0.004 0.053 1544 Dihedral : 8.283 72.861 1595 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.59 % Rotamer: Outliers : 3.36 % Allowed : 11.91 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.26), residues: 1134 helix: 1.05 (0.20), residues: 686 sheet: -0.21 (0.60), residues: 64 loop : -1.64 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 624 HIS 0.011 0.001 HIS B 457 PHE 0.018 0.001 PHE B 39 TYR 0.017 0.002 TYR A 276 ARG 0.017 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8439 (mttt) cc_final: 0.8187 (mttp) REVERT: A 222 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7824 (m-40) REVERT: A 242 ILE cc_start: 0.8531 (tp) cc_final: 0.8179 (pt) REVERT: A 243 HIS cc_start: 0.7598 (t70) cc_final: 0.7282 (t-90) REVERT: A 263 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7476 (mmt90) REVERT: A 265 MET cc_start: 0.7242 (mmt) cc_final: 0.7035 (mmp) REVERT: A 393 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7975 (pt0) REVERT: A 521 SER cc_start: 0.8949 (m) cc_final: 0.8677 (p) REVERT: B 71 MET cc_start: 0.7064 (mmt) cc_final: 0.6636 (mmt) REVERT: B 187 SER cc_start: 0.7909 (m) cc_final: 0.7617 (p) REVERT: B 190 GLU cc_start: 0.7135 (mp0) cc_final: 0.6690 (mp0) REVERT: B 261 SER cc_start: 0.8601 (m) cc_final: 0.8385 (t) REVERT: B 299 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7298 (m110) outliers start: 33 outliers final: 17 residues processed: 191 average time/residue: 0.2078 time to fit residues: 55.9823 Evaluate side-chains 158 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 622 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 457 HIS ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9355 Z= 0.219 Angle : 0.609 12.908 12703 Z= 0.316 Chirality : 0.042 0.197 1478 Planarity : 0.004 0.043 1544 Dihedral : 7.553 79.007 1595 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.75 % Allowed : 14.05 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.26), residues: 1134 helix: 1.39 (0.20), residues: 680 sheet: -0.16 (0.56), residues: 62 loop : -1.47 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 379 HIS 0.006 0.001 HIS B 457 PHE 0.013 0.001 PHE A 277 TYR 0.017 0.001 TYR A 413 ARG 0.007 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8448 (mttt) cc_final: 0.8174 (mttp) REVERT: A 207 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8301 (mt) REVERT: A 222 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7681 (m-40) REVERT: A 242 ILE cc_start: 0.8559 (tp) cc_final: 0.8109 (pt) REVERT: A 243 HIS cc_start: 0.7743 (t70) cc_final: 0.7377 (t-90) REVERT: A 263 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7508 (mmt90) REVERT: A 521 SER cc_start: 0.8949 (m) cc_final: 0.8609 (p) REVERT: B 71 MET cc_start: 0.7128 (mmt) cc_final: 0.6820 (mmt) REVERT: B 131 MET cc_start: 0.7163 (ttp) cc_final: 0.6946 (ttp) REVERT: B 187 SER cc_start: 0.7966 (m) cc_final: 0.7704 (p) REVERT: B 190 GLU cc_start: 0.7175 (mp0) cc_final: 0.6773 (mp0) outliers start: 27 outliers final: 20 residues processed: 169 average time/residue: 0.1916 time to fit residues: 46.7574 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9355 Z= 0.170 Angle : 0.566 11.215 12703 Z= 0.293 Chirality : 0.041 0.146 1478 Planarity : 0.004 0.038 1544 Dihedral : 6.988 89.684 1595 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.05 % Allowed : 15.17 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1134 helix: 1.57 (0.20), residues: 682 sheet: 0.08 (0.54), residues: 62 loop : -1.31 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 379 HIS 0.003 0.001 HIS B 243 PHE 0.016 0.001 PHE B 39 TYR 0.014 0.001 TYR A 413 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7104 (ptmm) REVERT: A 97 LYS cc_start: 0.8442 (mttt) cc_final: 0.8164 (mttp) REVERT: A 207 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8299 (mt) REVERT: A 222 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7593 (m-40) REVERT: A 243 HIS cc_start: 0.7722 (t70) cc_final: 0.7468 (t-90) REVERT: A 263 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7465 (mmt90) REVERT: A 343 LYS cc_start: 0.7770 (mptt) cc_final: 0.7471 (mppt) REVERT: A 552 SER cc_start: 0.9182 (t) cc_final: 0.8971 (p) REVERT: B 68 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.7190 (p0) REVERT: B 131 MET cc_start: 0.7112 (ttp) cc_final: 0.6892 (ttp) REVERT: B 187 SER cc_start: 0.7997 (m) cc_final: 0.7752 (t) REVERT: B 477 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7761 (m-30) outliers start: 30 outliers final: 18 residues processed: 158 average time/residue: 0.2051 time to fit residues: 46.0149 Evaluate side-chains 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 166 GLN B 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9355 Z= 0.302 Angle : 0.666 16.661 12703 Z= 0.341 Chirality : 0.043 0.168 1478 Planarity : 0.004 0.042 1544 Dihedral : 6.702 80.068 1595 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.38 % Allowed : 15.17 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.26), residues: 1134 helix: 1.34 (0.20), residues: 684 sheet: -0.02 (0.54), residues: 62 loop : -1.35 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 379 HIS 0.004 0.001 HIS B 267 PHE 0.018 0.002 PHE B 495 TYR 0.018 0.002 TYR B 413 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7125 (ptmm) REVERT: A 207 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 222 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7600 (m-40) REVERT: A 243 HIS cc_start: 0.7685 (t70) cc_final: 0.7429 (t-90) REVERT: A 263 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7619 (mmt90) REVERT: A 296 ASP cc_start: 0.7074 (m-30) cc_final: 0.6815 (m-30) REVERT: A 515 MET cc_start: 0.8785 (mmm) cc_final: 0.8485 (mmm) REVERT: B 131 MET cc_start: 0.7256 (ttp) cc_final: 0.7053 (ttp) REVERT: B 172 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8091 (mmtm) REVERT: B 214 THR cc_start: 0.7895 (m) cc_final: 0.7690 (t) REVERT: B 385 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 477 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7777 (m-30) outliers start: 43 outliers final: 28 residues processed: 166 average time/residue: 0.1984 time to fit residues: 47.3215 Evaluate side-chains 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 91 optimal weight: 0.0370 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 244 GLN B 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9355 Z= 0.168 Angle : 0.577 14.441 12703 Z= 0.295 Chirality : 0.040 0.178 1478 Planarity : 0.004 0.033 1544 Dihedral : 6.275 73.361 1595 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.56 % Allowed : 16.19 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.26), residues: 1134 helix: 1.67 (0.20), residues: 680 sheet: 0.37 (0.56), residues: 62 loop : -1.01 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 379 HIS 0.003 0.001 HIS B 267 PHE 0.018 0.001 PHE B 448 TYR 0.012 0.001 TYR A 413 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7141 (ptmm) REVERT: A 207 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8302 (mt) REVERT: A 222 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7549 (m110) REVERT: A 243 HIS cc_start: 0.7701 (t70) cc_final: 0.7449 (t-90) REVERT: A 263 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.7616 (mmt90) REVERT: A 296 ASP cc_start: 0.7053 (m-30) cc_final: 0.6798 (m-30) REVERT: A 343 LYS cc_start: 0.7774 (mptt) cc_final: 0.7352 (mppt) REVERT: B 90 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8235 (mm) REVERT: B 131 MET cc_start: 0.7178 (ttp) cc_final: 0.6968 (ttp) REVERT: B 172 LYS cc_start: 0.8274 (mtmm) cc_final: 0.8055 (mmtm) REVERT: B 214 THR cc_start: 0.7826 (m) cc_final: 0.7614 (t) REVERT: B 477 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7820 (m-30) outliers start: 35 outliers final: 26 residues processed: 153 average time/residue: 0.1964 time to fit residues: 43.3553 Evaluate side-chains 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 398 GLN B 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9355 Z= 0.190 Angle : 0.575 14.054 12703 Z= 0.294 Chirality : 0.040 0.147 1478 Planarity : 0.004 0.036 1544 Dihedral : 6.105 68.319 1595 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.87 % Allowed : 16.60 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.26), residues: 1134 helix: 1.69 (0.20), residues: 682 sheet: 0.62 (0.57), residues: 62 loop : -1.06 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 379 HIS 0.003 0.001 HIS B 267 PHE 0.020 0.001 PHE A 277 TYR 0.012 0.001 TYR A 413 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7143 (ptmm) REVERT: A 207 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8310 (mt) REVERT: A 222 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7683 (m-40) REVERT: A 243 HIS cc_start: 0.7704 (t70) cc_final: 0.7455 (t-90) REVERT: A 263 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7641 (mmt90) REVERT: A 296 ASP cc_start: 0.6942 (m-30) cc_final: 0.6696 (m-30) REVERT: A 343 LYS cc_start: 0.7773 (mptt) cc_final: 0.7464 (mppt) REVERT: A 515 MET cc_start: 0.8732 (mmm) cc_final: 0.8407 (mmm) REVERT: B 172 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8055 (mmtm) REVERT: B 214 THR cc_start: 0.7879 (m) cc_final: 0.7671 (t) REVERT: B 477 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7898 (m-30) outliers start: 38 outliers final: 29 residues processed: 153 average time/residue: 0.2126 time to fit residues: 46.3713 Evaluate side-chains 154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9355 Z= 0.157 Angle : 0.548 13.164 12703 Z= 0.280 Chirality : 0.039 0.145 1478 Planarity : 0.004 0.046 1544 Dihedral : 5.814 61.028 1595 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.67 % Allowed : 17.01 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.26), residues: 1134 helix: 1.81 (0.20), residues: 686 sheet: 1.00 (0.58), residues: 62 loop : -1.14 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 379 HIS 0.002 0.000 HIS B 267 PHE 0.017 0.001 PHE B 448 TYR 0.011 0.001 TYR A 282 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8308 (mt) REVERT: A 243 HIS cc_start: 0.7710 (t70) cc_final: 0.7425 (t-90) REVERT: A 263 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7641 (mmt90) REVERT: A 343 LYS cc_start: 0.7859 (mptt) cc_final: 0.7568 (mppt) REVERT: B 172 LYS cc_start: 0.8262 (mtmm) cc_final: 0.8046 (mmtm) REVERT: B 214 THR cc_start: 0.7918 (m) cc_final: 0.7671 (t) REVERT: B 385 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6499 (t80) outliers start: 36 outliers final: 30 residues processed: 159 average time/residue: 0.2260 time to fit residues: 50.8861 Evaluate side-chains 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9355 Z= 0.299 Angle : 0.662 12.413 12703 Z= 0.339 Chirality : 0.043 0.153 1478 Planarity : 0.004 0.042 1544 Dihedral : 6.104 58.804 1595 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.77 % Allowed : 18.13 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.26), residues: 1134 helix: 1.49 (0.20), residues: 688 sheet: 0.68 (0.52), residues: 88 loop : -1.38 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 624 HIS 0.004 0.001 HIS B 267 PHE 0.018 0.002 PHE A 277 TYR 0.016 0.002 TYR B 413 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8290 (mt) REVERT: A 243 HIS cc_start: 0.7713 (t70) cc_final: 0.7451 (t-90) REVERT: A 263 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.7151 (mpp-170) REVERT: B 172 LYS cc_start: 0.8313 (mtmm) cc_final: 0.8069 (mmtm) REVERT: B 385 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6784 (t80) outliers start: 37 outliers final: 25 residues processed: 151 average time/residue: 0.2072 time to fit residues: 44.5734 Evaluate side-chains 145 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9355 Z= 0.185 Angle : 0.606 11.663 12703 Z= 0.310 Chirality : 0.040 0.186 1478 Planarity : 0.004 0.054 1544 Dihedral : 5.838 54.996 1595 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.05 % Allowed : 19.14 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1134 helix: 1.67 (0.20), residues: 688 sheet: 0.95 (0.58), residues: 62 loop : -1.14 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 379 HIS 0.017 0.001 HIS A 155 PHE 0.019 0.001 PHE A 277 TYR 0.013 0.001 TYR B 463 ARG 0.007 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7196 (ptmm) REVERT: A 207 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8293 (mt) REVERT: A 243 HIS cc_start: 0.7715 (t70) cc_final: 0.7470 (t-90) REVERT: A 263 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7641 (mmt90) REVERT: A 343 LYS cc_start: 0.7745 (mptt) cc_final: 0.7514 (mppt) REVERT: A 515 MET cc_start: 0.8737 (mmm) cc_final: 0.8435 (mmm) REVERT: B 172 LYS cc_start: 0.8274 (mtmm) cc_final: 0.8054 (mmtm) REVERT: B 385 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6676 (t80) outliers start: 30 outliers final: 24 residues processed: 149 average time/residue: 0.2055 time to fit residues: 43.6067 Evaluate side-chains 148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 79 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.119467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102125 restraints weight = 17289.847| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.97 r_work: 0.3303 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9355 Z= 0.241 Angle : 0.628 10.292 12703 Z= 0.322 Chirality : 0.041 0.157 1478 Planarity : 0.004 0.052 1544 Dihedral : 5.847 51.489 1595 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.16 % Allowed : 19.25 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.26), residues: 1134 helix: 1.75 (0.20), residues: 670 sheet: 0.81 (0.52), residues: 88 loop : -0.94 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.003 0.001 HIS B 267 PHE 0.024 0.001 PHE B 39 TYR 0.014 0.001 TYR B 413 ARG 0.007 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.80 seconds wall clock time: 37 minutes 32.35 seconds (2252.35 seconds total)