Starting phenix.real_space_refine on Fri Mar 14 03:38:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oj8_12939/03_2025/7oj8_12939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oj8_12939/03_2025/7oj8_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_12939/03_2025/7oj8_12939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oj8_12939/03_2025/7oj8_12939.map" model { file = "/net/cci-nas-00/data/ceres_data/7oj8_12939/03_2025/7oj8_12939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oj8_12939/03_2025/7oj8_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-5624/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: 6.49, per 1000 atoms: 0.71 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: 2.60 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: 0.97 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: 2.47 Time building geometry restraints manager: 3.05 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: 1.770 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.610 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- 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 : 0.940 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: 0.2253 time to fit residues: 80.3795 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 : 0.927 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106890 restraints weight = 16702.680| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.84 r_work: 0.3400 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8608 (mttt) cc_final: 0.8331 (mttp) REVERT: A 222 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7823 (m-40) REVERT: A 242 ILE cc_start: 0.8549 (tp) cc_final: 0.8199 (pt) REVERT: A 243 HIS cc_start: 0.7771 (t70) cc_final: 0.7479 (t-90) REVERT: A 263 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7839 (mmt90) REVERT: A 265 MET cc_start: 0.7515 (mmt) cc_final: 0.7299 (mmp) REVERT: A 296 ASP cc_start: 0.7635 (m-30) cc_final: 0.7433 (m-30) REVERT: A 393 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8014 (pt0) REVERT: A 521 SER cc_start: 0.9046 (m) cc_final: 0.8768 (p) REVERT: B 71 MET cc_start: 0.7313 (mmt) cc_final: 0.6894 (mmt) REVERT: B 187 SER cc_start: 0.8034 (m) cc_final: 0.7693 (p) REVERT: B 190 GLU cc_start: 0.7301 (mp0) cc_final: 0.6879 (mp0) REVERT: B 261 SER cc_start: 0.8759 (m) cc_final: 0.8541 (t) REVERT: B 299 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7257 (m110) REVERT: B 483 MET cc_start: 0.8467 (tmm) cc_final: 0.8194 (ttm) outliers start: 33 outliers final: 17 residues processed: 191 average time/residue: 0.2013 time to fit residues: 54.3935 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 : 0.959 ------------------------------------------------------------------------------- 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 109 optimal weight: 8.9990 chunk 49 optimal weight: 0.0770 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.121248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104083 restraints weight = 17201.509| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.09 r_work: 0.3323 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3132 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= 0.206 Angle : 0.604 12.933 12703 Z= 0.313 Chirality : 0.042 0.197 1478 Planarity : 0.004 0.043 1544 Dihedral : 7.527 78.824 1595 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.55 % Allowed : 14.46 % Favored : 82.99 % 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: 0.52 (0.26), residues: 1134 helix: 1.39 (0.20), residues: 680 sheet: -0.13 (0.57), residues: 62 loop : -1.46 (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 0.008 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 177 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8504 (mttt) cc_final: 0.8126 (mttp) REVERT: A 207 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8206 (mt) REVERT: A 222 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7364 (m-40) REVERT: A 242 ILE cc_start: 0.8411 (tp) cc_final: 0.7968 (pt) REVERT: A 243 HIS cc_start: 0.7960 (t70) cc_final: 0.7610 (t-90) REVERT: A 263 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7634 (mmt90) REVERT: A 296 ASP cc_start: 0.7530 (m-30) cc_final: 0.7254 (m-30) REVERT: A 496 MET cc_start: 0.8241 (ttp) cc_final: 0.7599 (ttp) REVERT: A 521 SER cc_start: 0.8885 (m) cc_final: 0.8509 (p) REVERT: A 572 SER cc_start: 0.8430 (m) cc_final: 0.8171 (p) REVERT: B 71 MET cc_start: 0.7401 (mmt) cc_final: 0.6944 (mmt) REVERT: B 131 MET cc_start: 0.7202 (ttp) cc_final: 0.6930 (ttp) REVERT: B 187 SER cc_start: 0.8095 (m) cc_final: 0.7736 (p) REVERT: B 190 GLU cc_start: 0.7307 (mp0) cc_final: 0.6891 (mp0) REVERT: B 261 SER cc_start: 0.8687 (m) cc_final: 0.8461 (t) REVERT: B 265 MET cc_start: 0.6859 (mmt) cc_final: 0.5801 (mmt) outliers start: 25 outliers final: 19 residues processed: 169 average time/residue: 0.2308 time to fit residues: 55.4427 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 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 458 GLU 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 92 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 166 GLN B 244 GLN B 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098758 restraints weight = 17510.395| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.03 r_work: 0.3245 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9355 Z= 0.398 Angle : 0.713 16.056 12703 Z= 0.371 Chirality : 0.047 0.214 1478 Planarity : 0.004 0.041 1544 Dihedral : 7.341 85.741 1595 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.58 % Allowed : 14.15 % Favored : 81.26 % 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: 0.11 (0.25), residues: 1134 helix: 1.05 (0.20), residues: 684 sheet: -0.68 (0.52), residues: 82 loop : -1.57 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 624 HIS 0.007 0.001 HIS B 267 PHE 0.021 0.002 PHE B 495 TYR 0.018 0.002 TYR B 413 ARG 0.006 0.001 ARG A 147 *********************** 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 185 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6953 (ptmm) REVERT: A 97 LYS cc_start: 0.8607 (mttt) cc_final: 0.8209 (mttp) REVERT: A 222 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7272 (m-40) REVERT: A 243 HIS cc_start: 0.8016 (t70) cc_final: 0.7808 (t-90) REVERT: A 263 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7871 (mmt90) REVERT: A 296 ASP cc_start: 0.7485 (m-30) cc_final: 0.7178 (m-30) REVERT: A 496 MET cc_start: 0.8350 (ttp) cc_final: 0.7664 (ttp) REVERT: A 515 MET cc_start: 0.9057 (mmm) cc_final: 0.8743 (mmm) REVERT: A 521 SER cc_start: 0.8913 (m) cc_final: 0.8693 (p) REVERT: B 71 MET cc_start: 0.7718 (mmt) cc_final: 0.7414 (mmt) REVERT: B 187 SER cc_start: 0.8280 (m) cc_final: 0.7912 (t) REVERT: B 190 GLU cc_start: 0.7478 (mp0) cc_final: 0.7221 (mp0) REVERT: B 385 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6482 (t80) outliers start: 45 outliers final: 29 residues processed: 170 average time/residue: 0.2417 time to fit residues: 59.0784 Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 225 LEU 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 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 493 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 244 GLN 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 458 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100925 restraints weight = 17266.093| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.06 r_work: 0.3277 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9355 Z= 0.247 Angle : 0.629 14.617 12703 Z= 0.326 Chirality : 0.042 0.153 1478 Planarity : 0.004 0.039 1544 Dihedral : 6.889 79.631 1595 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.18 % Allowed : 16.09 % Favored : 79.74 % 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: 0.62 (0.26), residues: 1134 helix: 1.45 (0.20), residues: 666 sheet: -0.39 (0.50), residues: 82 loop : -1.23 (0.35), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 379 HIS 0.004 0.001 HIS B 267 PHE 0.018 0.001 PHE B 448 TYR 0.024 0.002 TYR A 605 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 171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.6978 (ptmm) REVERT: A 207 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8209 (mt) REVERT: A 222 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7267 (m110) REVERT: A 263 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7053 (mpp-170) REVERT: A 296 ASP cc_start: 0.7548 (m-30) cc_final: 0.7231 (m-30) REVERT: A 343 LYS cc_start: 0.7764 (mptt) cc_final: 0.7410 (mppt) REVERT: A 438 CYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8936 (t) REVERT: A 496 MET cc_start: 0.8308 (ttp) cc_final: 0.7568 (ttp) REVERT: A 521 SER cc_start: 0.8921 (m) cc_final: 0.8694 (p) REVERT: B 39 PHE cc_start: 0.8263 (p90) cc_final: 0.8034 (p90) REVERT: B 71 MET cc_start: 0.7622 (mmt) cc_final: 0.7345 (mmt) REVERT: B 172 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7911 (mmtm) REVERT: B 187 SER cc_start: 0.8312 (m) cc_final: 0.7938 (t) REVERT: B 190 GLU cc_start: 0.7392 (mp0) cc_final: 0.7145 (mp0) REVERT: B 385 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6387 (t80) REVERT: B 477 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7696 (m-30) outliers start: 41 outliers final: 24 residues processed: 156 average time/residue: 0.2036 time to fit residues: 45.6820 Evaluate side-chains 156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 225 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 438 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 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 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 106 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 398 GLN B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104971 restraints weight = 17207.447| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.98 r_work: 0.3346 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9355 Z= 0.169 Angle : 0.584 14.241 12703 Z= 0.299 Chirality : 0.040 0.151 1478 Planarity : 0.004 0.036 1544 Dihedral : 6.402 72.876 1595 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.46 % Allowed : 17.01 % 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: 0.82 (0.26), residues: 1134 helix: 1.56 (0.20), residues: 678 sheet: 0.17 (0.56), residues: 62 loop : -1.19 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 379 HIS 0.006 0.001 HIS B 243 PHE 0.016 0.001 PHE B 448 TYR 0.012 0.001 TYR A 605 ARG 0.007 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 176 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7037 (ptmm) REVERT: A 207 LEU cc_start: 0.8719 (mt) cc_final: 0.8380 (mt) REVERT: A 222 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7378 (m-40) REVERT: A 263 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7899 (mmt90) REVERT: A 496 MET cc_start: 0.7964 (ttp) cc_final: 0.7540 (ttp) REVERT: A 515 MET cc_start: 0.8909 (mmm) cc_final: 0.8596 (mmm) REVERT: A 521 SER cc_start: 0.8981 (m) cc_final: 0.8685 (p) REVERT: B 71 MET cc_start: 0.7601 (mmt) cc_final: 0.7382 (mmt) REVERT: B 172 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7968 (mmtm) REVERT: B 187 SER cc_start: 0.8295 (m) cc_final: 0.7926 (t) REVERT: B 328 LEU cc_start: 0.7811 (tp) cc_final: 0.7496 (mp) REVERT: B 418 ASN cc_start: 0.7903 (p0) cc_final: 0.7636 (p0) outliers start: 34 outliers final: 24 residues processed: 165 average time/residue: 0.1895 time to fit residues: 45.0040 Evaluate side-chains 148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 445 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 533 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 198 MET 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 0.0050 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 350 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.100167 restraints weight = 17652.737| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.96 r_work: 0.3271 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4312 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= 0.303 Angle : 0.663 12.942 12703 Z= 0.339 Chirality : 0.043 0.152 1478 Planarity : 0.004 0.041 1544 Dihedral : 6.495 68.307 1595 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.18 % Allowed : 16.80 % Favored : 79.02 % 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: 0.72 (0.26), residues: 1134 helix: 1.46 (0.20), residues: 670 sheet: 0.07 (0.52), residues: 88 loop : -1.21 (0.35), residues: 376 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 0.019 0.002 PHE A 277 TYR 0.015 0.002 TYR B 413 ARG 0.009 0.001 ARG A 163 *********************** 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 174 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7051 (ptmm) REVERT: A 207 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8374 (mt) REVERT: A 263 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7231 (mpp-170) REVERT: A 343 LYS cc_start: 0.7775 (mptt) cc_final: 0.7409 (mppt) REVERT: A 496 MET cc_start: 0.8253 (ttp) cc_final: 0.7739 (ttp) REVERT: A 515 MET cc_start: 0.8996 (mmm) cc_final: 0.8692 (mmm) REVERT: A 521 SER cc_start: 0.9039 (m) cc_final: 0.8719 (p) REVERT: A 541 MET cc_start: 0.8448 (mmm) cc_final: 0.8237 (mtp) REVERT: B 172 LYS cc_start: 0.8325 (mtmm) cc_final: 0.8007 (mmtm) REVERT: B 328 LEU cc_start: 0.7741 (tp) cc_final: 0.7428 (mp) REVERT: B 385 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6621 (t80) REVERT: B 418 ASN cc_start: 0.8139 (p0) cc_final: 0.7800 (p0) outliers start: 41 outliers final: 26 residues processed: 165 average time/residue: 0.2882 time to fit residues: 70.9427 Evaluate side-chains 150 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 178 VAL Chi-restraints excluded: chain A residue 207 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 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 105 ASP 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 458 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104648 restraints weight = 17559.825| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.01 r_work: 0.3312 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4490 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= 0.181 Angle : 0.609 12.982 12703 Z= 0.306 Chirality : 0.040 0.153 1478 Planarity : 0.003 0.036 1544 Dihedral : 6.119 62.897 1595 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.36 % Allowed : 18.33 % Favored : 78.31 % 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: 1.14 (0.26), residues: 1134 helix: 1.80 (0.20), residues: 664 sheet: 0.60 (0.59), residues: 62 loop : -0.99 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 379 HIS 0.003 0.001 HIS B 267 PHE 0.021 0.001 PHE B 39 TYR 0.021 0.001 TYR B 276 ARG 0.006 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 165 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6981 (ptmm) REVERT: A 207 LEU cc_start: 0.8634 (mt) cc_final: 0.8323 (mt) REVERT: A 263 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7818 (mmt90) REVERT: A 343 LYS cc_start: 0.7790 (mptt) cc_final: 0.7402 (mppt) REVERT: A 521 SER cc_start: 0.9012 (m) cc_final: 0.8694 (p) REVERT: A 541 MET cc_start: 0.8431 (mmm) cc_final: 0.8108 (mtp) REVERT: B 37 LEU cc_start: 0.7953 (tt) cc_final: 0.7723 (tt) REVERT: B 172 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7972 (mmtm) REVERT: B 328 LEU cc_start: 0.7779 (tp) cc_final: 0.7446 (mp) REVERT: B 385 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6611 (t80) REVERT: B 418 ASN cc_start: 0.8024 (p0) cc_final: 0.7708 (p0) outliers start: 33 outliers final: 26 residues processed: 159 average time/residue: 0.3818 time to fit residues: 88.6717 Evaluate side-chains 147 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 CYS 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 B residue 105 ASP 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 458 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101441 restraints weight = 17731.887| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.06 r_work: 0.3303 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9355 Z= 0.181 Angle : 0.598 11.606 12703 Z= 0.300 Chirality : 0.039 0.149 1478 Planarity : 0.004 0.037 1544 Dihedral : 5.874 56.226 1595 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.26 % Allowed : 18.64 % 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: 1.04 (0.26), residues: 1134 helix: 1.73 (0.20), residues: 678 sheet: 0.85 (0.60), residues: 62 loop : -1.23 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 379 HIS 0.002 0.001 HIS B 267 PHE 0.014 0.001 PHE A 277 TYR 0.019 0.001 TYR B 276 ARG 0.007 0.000 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 159 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.8562 (mt) cc_final: 0.8292 (mt) REVERT: A 263 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7786 (mmt90) REVERT: A 343 LYS cc_start: 0.7780 (mptt) cc_final: 0.7379 (mppt) REVERT: A 521 SER cc_start: 0.9009 (m) cc_final: 0.8669 (p) REVERT: B 37 LEU cc_start: 0.7834 (tt) cc_final: 0.7620 (tt) REVERT: B 172 LYS cc_start: 0.8319 (mtmm) cc_final: 0.7967 (mmtm) REVERT: B 243 HIS cc_start: 0.6927 (m170) cc_final: 0.6720 (m170) REVERT: B 328 LEU cc_start: 0.7790 (tp) cc_final: 0.7448 (mp) REVERT: B 385 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6765 (t80) REVERT: B 418 ASN cc_start: 0.8058 (p0) cc_final: 0.7743 (p0) outliers start: 32 outliers final: 27 residues processed: 154 average time/residue: 0.2042 time to fit residues: 45.6113 Evaluate side-chains 149 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 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 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 474 LEU 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 B residue 105 ASP 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 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 466 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 68 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 222 ASN A 283 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.118145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.101385 restraints weight = 17911.956| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.12 r_work: 0.3310 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9355 Z= 0.184 Angle : 0.605 10.601 12703 Z= 0.303 Chirality : 0.040 0.207 1478 Planarity : 0.004 0.036 1544 Dihedral : 5.723 51.892 1595 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.85 % Allowed : 19.25 % Favored : 77.90 % 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: 1.08 (0.26), residues: 1134 helix: 1.79 (0.21), residues: 680 sheet: 0.99 (0.59), residues: 62 loop : -1.31 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 379 HIS 0.014 0.001 HIS A 155 PHE 0.025 0.001 PHE B 39 TYR 0.019 0.001 TYR B 276 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 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.8563 (mt) cc_final: 0.8308 (mt) REVERT: A 263 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7794 (mmt90) REVERT: A 343 LYS cc_start: 0.7782 (mptt) cc_final: 0.7529 (mppt) REVERT: A 515 MET cc_start: 0.8991 (mmm) cc_final: 0.8696 (mmm) REVERT: A 521 SER cc_start: 0.9013 (m) cc_final: 0.8665 (p) REVERT: B 37 LEU cc_start: 0.7756 (tt) cc_final: 0.7536 (tt) REVERT: B 172 LYS cc_start: 0.8300 (mtmm) cc_final: 0.7965 (mmtm) REVERT: B 243 HIS cc_start: 0.7053 (m170) cc_final: 0.6848 (m170) REVERT: B 328 LEU cc_start: 0.7776 (tp) cc_final: 0.7440 (mp) REVERT: B 385 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6753 (t80) REVERT: B 418 ASN cc_start: 0.8021 (p0) cc_final: 0.7707 (p0) outliers start: 28 outliers final: 22 residues processed: 148 average time/residue: 0.1920 time to fit residues: 40.9515 Evaluate side-chains 146 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 178 VAL 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 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 590 ASN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ASN 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 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 466 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 32 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100646 restraints weight = 17886.724| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.11 r_work: 0.3306 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 9355 Z= 0.272 Angle : 0.904 59.198 12703 Z= 0.533 Chirality : 0.046 0.782 1478 Planarity : 0.004 0.056 1544 Dihedral : 5.787 51.912 1595 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.50 % Rotamer: Outliers : 2.75 % Allowed : 19.65 % Favored : 77.60 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.01 (0.26), residues: 1134 helix: 1.72 (0.21), residues: 680 sheet: 1.01 (0.59), residues: 62 loop : -1.32 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.015 0.001 PHE A 277 TYR 0.017 0.001 TYR B 276 ARG 0.006 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3843.49 seconds wall clock time: 70 minutes 41.67 seconds (4241.67 seconds total)