Starting phenix.real_space_refine on Mon Jun 16 19:23:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chs_45600/06_2025/9chs_45600.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chs_45600/06_2025/9chs_45600.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/9chs_45600/06_2025/9chs_45600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chs_45600/06_2025/9chs_45600.map" model { file = "/net/cci-nas-00/data/ceres_data/9chs_45600/06_2025/9chs_45600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chs_45600/06_2025/9chs_45600.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= 0.000 sd= 0.004 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 S 48 5.16 5 C 6292 2.51 5 N 1568 2.21 5 O 1600 1.98 5 H 9596 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19104 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Chain: "B" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Chain: "C" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Chain: "D" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Time building chain proxies: 9.90, per 1000 atoms: 0.52 Number of scatterers: 19104 At special positions: 0 Unit cell: (123.9, 122.85, 96.6, 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 48 16.00 O 1600 8.00 N 1568 7.00 C 6292 6.00 H 9596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 404 through 432 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.897A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.748A pdb=" N LEU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.918A pdb=" N VAL A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 576 Processing helix chain 'A' and resid 584 through 593 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.593A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 688 Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.042A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 432 removed outlier: 3.638A pdb=" N LEU B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 471 removed outlier: 3.626A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 495 Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.733A pdb=" N LYS B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.796A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 545 through 574 removed outlier: 3.653A pdb=" N PHE B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.660A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 687 Processing helix chain 'B' and resid 690 through 709 removed outlier: 4.163A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 432 removed outlier: 3.851A pdb=" N LEU C 416 " --> pdb=" O TRP C 412 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 471 removed outlier: 3.803A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 495 Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 507 through 511 Processing helix chain 'C' and resid 517 through 525 removed outlier: 3.960A pdb=" N ILE C 521 " --> pdb=" O SER C 517 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 525 " --> pdb=" O ILE C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 574 removed outlier: 3.679A pdb=" N PHE C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.642A pdb=" N GLY C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 688 removed outlier: 3.534A pdb=" N ARG C 672 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.505A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 432 removed outlier: 3.799A pdb=" N LEU D 416 " --> pdb=" O TRP D 412 " (cutoff:3.500A) Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 471 removed outlier: 4.251A pdb=" N ASP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 495 Processing helix chain 'D' and resid 497 through 504 Processing helix chain 'D' and resid 505 through 506 No H-bonds generated for 'chain 'D' and resid 505 through 506' Processing helix chain 'D' and resid 507 through 511 Processing helix chain 'D' and resid 517 through 525 removed outlier: 3.888A pdb=" N LEU D 523 " --> pdb=" O GLU D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 574 Processing helix chain 'D' and resid 584 through 593 Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 634 through 653 Processing helix chain 'D' and resid 654 through 667 Processing helix chain 'D' and resid 667 through 688 Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.701A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR D 700 " --> pdb=" O ARG D 696 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1950 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: 6.46 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9580 1.13 - 1.30: 1520 1.30 - 1.48: 4058 1.48 - 1.65: 4134 1.65 - 1.82: 80 Bond restraints: 19372 Sorted by residual: bond pdb=" N ALA B 527 " pdb=" H ALA B 527 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CZ2 TRP D 585 " pdb=" HZ2 TRP D 585 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N PHE C 471 " pdb=" H PHE C 471 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD1 TRP A 412 " pdb=" HD1 TRP A 412 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 HIS B 492 " pdb=" HD2 HIS B 492 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 19367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 29901 2.62 - 5.24: 3865 5.24 - 7.86: 1115 7.86 - 10.49: 15 10.49 - 13.11: 16 Bond angle restraints: 34912 Sorted by residual: angle pdb=" CA ASN B 629 " pdb=" CB ASN B 629 " pdb=" CG ASN B 629 " ideal model delta sigma weight residual 112.60 117.58 -4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" CB HIS D 485 " pdb=" CG HIS D 485 " pdb=" CD2 HIS D 485 " ideal model delta sigma weight residual 131.20 124.83 6.37 1.30e+00 5.92e-01 2.40e+01 angle pdb=" CB HIS B 578 " pdb=" CG HIS B 578 " pdb=" CD2 HIS B 578 " ideal model delta sigma weight residual 131.20 124.84 6.36 1.30e+00 5.92e-01 2.39e+01 angle pdb=" CB HIS D 578 " pdb=" CG HIS D 578 " pdb=" CD2 HIS D 578 " ideal model delta sigma weight residual 131.20 124.88 6.32 1.30e+00 5.92e-01 2.36e+01 angle pdb=" CA ASN C 629 " pdb=" CB ASN C 629 " pdb=" CG ASN C 629 " ideal model delta sigma weight residual 112.60 117.39 -4.79 1.00e+00 1.00e+00 2.29e+01 ... (remaining 34907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 8550 17.67 - 35.35: 383 35.35 - 53.02: 108 53.02 - 70.69: 78 70.69 - 88.37: 5 Dihedral angle restraints: 9124 sinusoidal: 4760 harmonic: 4364 Sorted by residual: dihedral pdb=" CA LEU A 510 " pdb=" C LEU A 510 " pdb=" N LEU A 511 " pdb=" CA LEU A 511 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA VAL B 476 " pdb=" C VAL B 476 " pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PHE B 656 " pdb=" C PHE B 656 " pdb=" N GLY B 657 " pdb=" CA GLY B 657 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 887 0.073 - 0.146: 483 0.146 - 0.218: 100 0.218 - 0.291: 15 0.291 - 0.364: 11 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA SER C 624 " pdb=" N SER C 624 " pdb=" C SER C 624 " pdb=" CB SER C 624 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA SER A 624 " pdb=" N SER A 624 " pdb=" C SER A 624 " pdb=" CB SER A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA SER B 624 " pdb=" N SER B 624 " pdb=" C SER B 624 " pdb=" CB SER B 624 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1493 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 545 " 0.139 2.00e-02 2.50e+03 6.48e-02 1.26e+02 pdb=" CG TYR A 545 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 545 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 545 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 545 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR A 545 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR A 545 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 545 " 0.146 2.00e-02 2.50e+03 pdb=" HD1 TYR A 545 " -0.026 2.00e-02 2.50e+03 pdb=" HD2 TYR A 545 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 TYR A 545 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 545 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 534 " 0.411 9.50e-02 1.11e+02 1.52e-01 1.15e+02 pdb=" NE ARG A 534 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 534 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 534 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 534 " -0.014 2.00e-02 2.50e+03 pdb="HH11 ARG A 534 " -0.153 2.00e-02 2.50e+03 pdb="HH12 ARG A 534 " 0.072 2.00e-02 2.50e+03 pdb="HH21 ARG A 534 " -0.046 2.00e-02 2.50e+03 pdb="HH22 ARG A 534 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 528 " -0.219 9.50e-02 1.11e+02 9.97e-02 1.09e+02 pdb=" NE ARG B 528 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B 528 " 0.057 2.00e-02 2.50e+03 pdb=" NH1 ARG B 528 " 0.050 2.00e-02 2.50e+03 pdb=" NH2 ARG B 528 " 0.109 2.00e-02 2.50e+03 pdb="HH11 ARG B 528 " -0.036 2.00e-02 2.50e+03 pdb="HH12 ARG B 528 " -0.076 2.00e-02 2.50e+03 pdb="HH21 ARG B 528 " -0.127 2.00e-02 2.50e+03 pdb="HH22 ARG B 528 " 0.026 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 986 2.20 - 2.80: 34165 2.80 - 3.40: 52429 3.40 - 4.00: 68827 4.00 - 4.60: 98107 Nonbonded interactions: 254514 Sorted by model distance: nonbonded pdb=" OE2 GLU C 575 " pdb=" HG SER C 636 " model vdw 1.604 2.450 nonbonded pdb=" HG SER D 620 " pdb=" O VAL D 625 " model vdw 1.608 2.450 nonbonded pdb=" HG SER A 620 " pdb=" O VAL A 625 " model vdw 1.609 2.450 nonbonded pdb=" OE2 GLU D 575 " pdb=" HG SER D 636 " model vdw 1.609 2.450 nonbonded pdb=" HG SER B 620 " pdb=" O VAL B 625 " model vdw 1.611 2.450 ... (remaining 254509 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 54.640 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: 0.320 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 42.060 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.013 0.043 9776 Z= 0.762 Angle : 1.701 7.284 13288 Z= 1.180 Chirality : 0.089 0.364 1496 Planarity : 0.016 0.149 1620 Dihedral : 11.670 88.366 3420 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.93 (0.23), residues: 1140 helix: -0.67 (0.15), residues: 880 sheet: None (None), residues: 0 loop : 0.33 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.014 TRP B 585 HIS 0.010 0.002 HIS A 587 PHE 0.075 0.011 PHE C 701 TYR 0.135 0.024 TYR A 545 ARG 0.007 0.001 ARG C 681 Details of bonding type rmsd hydrogen bonds : bond 0.16580 ( 667) hydrogen bonds : angle 7.03064 ( 1950) covalent geometry : bond 0.01283 ( 9776) covalent geometry : angle 1.70141 (13288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.7732 (mmm) cc_final: 0.7418 (ppp) REVERT: A 662 ILE cc_start: 0.7941 (mm) cc_final: 0.7726 (mm) REVERT: A 677 MET cc_start: 0.7953 (tpp) cc_final: 0.7749 (tpp) REVERT: A 690 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.8027 (Cg_endo) REVERT: A 701 PHE cc_start: 0.8312 (t80) cc_final: 0.8066 (t80) REVERT: B 457 LEU cc_start: 0.7534 (tp) cc_final: 0.7244 (tt) REVERT: B 540 ASP cc_start: 0.8003 (p0) cc_final: 0.7638 (m-30) REVERT: C 673 TYR cc_start: 0.7713 (t80) cc_final: 0.7370 (t80) REVERT: C 677 MET cc_start: 0.6611 (tpp) cc_final: 0.5941 (ttp) REVERT: C 678 LEU cc_start: 0.8280 (mt) cc_final: 0.7978 (tt) REVERT: C 694 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7196 (ttt180) REVERT: D 462 MET cc_start: 0.7537 (mtp) cc_final: 0.7148 (mtp) REVERT: D 691 ASN cc_start: 0.8232 (t0) cc_final: 0.8018 (t0) REVERT: D 696 ARG cc_start: 0.7274 (mtp180) cc_final: 0.6697 (tmt170) REVERT: D 699 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7222 (mt-10) REVERT: D 703 HIS cc_start: 0.7967 (t-90) cc_final: 0.7710 (t70) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.6308 time to fit residues: 208.5499 Evaluate side-chains 193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS A 695 GLN B 573 ASN B 674 HIS C 485 HIS C 691 ASN D 687 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.167619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.115913 restraints weight = 31242.559| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.44 r_work: 0.2921 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9776 Z= 0.142 Angle : 0.549 5.027 13288 Z= 0.307 Chirality : 0.040 0.145 1496 Planarity : 0.004 0.036 1620 Dihedral : 4.570 18.350 1280 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.57 % Allowed : 4.12 % Favored : 94.31 % 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: 1.25 (0.25), residues: 1140 helix: 0.99 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.65 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.005 0.001 HIS C 485 PHE 0.014 0.001 PHE B 701 TYR 0.014 0.002 TYR B 611 ARG 0.003 0.001 ARG D 541 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 667) hydrogen bonds : angle 4.43010 ( 1950) covalent geometry : bond 0.00290 ( 9776) covalent geometry : angle 0.54925 (13288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6168 (tp) REVERT: A 574 MET cc_start: 0.8635 (mtt) cc_final: 0.8401 (mtp) REVERT: A 651 MET cc_start: 0.7455 (mmm) cc_final: 0.6826 (ppp) REVERT: A 677 MET cc_start: 0.8102 (tpp) cc_final: 0.7728 (tpt) REVERT: A 679 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.7065 (ttm-80) REVERT: A 690 PRO cc_start: 0.7856 (Cg_exo) cc_final: 0.7610 (Cg_endo) REVERT: A 698 GLU cc_start: 0.8397 (pt0) cc_final: 0.8174 (pt0) REVERT: B 457 LEU cc_start: 0.7323 (tp) cc_final: 0.7022 (tt) REVERT: B 540 ASP cc_start: 0.7893 (p0) cc_final: 0.7608 (m-30) REVERT: B 550 LEU cc_start: 0.8317 (mt) cc_final: 0.8108 (tt) REVERT: C 644 VAL cc_start: 0.9132 (t) cc_final: 0.8883 (t) REVERT: C 673 TYR cc_start: 0.7530 (t80) cc_final: 0.7293 (t80) REVERT: C 677 MET cc_start: 0.6774 (tpp) cc_final: 0.5947 (ttp) REVERT: C 678 LEU cc_start: 0.8420 (mt) cc_final: 0.8078 (tt) REVERT: C 679 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.7042 (tpt-90) REVERT: C 685 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7547 (mtm110) REVERT: D 449 CYS cc_start: 0.4333 (m) cc_final: 0.4007 (t) REVERT: D 462 MET cc_start: 0.7523 (mtp) cc_final: 0.7210 (mtt) REVERT: D 554 MET cc_start: 0.8200 (mmm) cc_final: 0.7992 (mmm) REVERT: D 696 ARG cc_start: 0.7481 (mtp180) cc_final: 0.6743 (tmt170) REVERT: D 699 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7166 (mt-10) outliers start: 16 outliers final: 12 residues processed: 223 average time/residue: 0.5882 time to fit residues: 182.0226 Evaluate side-chains 205 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 ASN B 709 ASN C 691 ASN C 709 ASN D 709 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.163248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.106172 restraints weight = 31368.197| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.03 r_work: 0.2856 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9776 Z= 0.241 Angle : 0.575 4.938 13288 Z= 0.323 Chirality : 0.042 0.158 1496 Planarity : 0.005 0.045 1620 Dihedral : 4.350 17.806 1280 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.86 % Allowed : 7.16 % Favored : 90.98 % 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: 1.34 (0.25), residues: 1140 helix: 1.07 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.62 (0.46), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 568 HIS 0.005 0.001 HIS B 687 PHE 0.019 0.002 PHE B 656 TYR 0.015 0.002 TYR A 427 ARG 0.005 0.001 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 667) hydrogen bonds : angle 4.42725 ( 1950) covalent geometry : bond 0.00552 ( 9776) covalent geometry : angle 0.57505 (13288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 MET cc_start: 0.8157 (tpp) cc_final: 0.7830 (tpp) REVERT: A 688 GLN cc_start: 0.8620 (mp10) cc_final: 0.8145 (mp10) REVERT: A 690 PRO cc_start: 0.8175 (Cg_exo) cc_final: 0.7896 (Cg_endo) REVERT: A 701 PHE cc_start: 0.8430 (t80) cc_final: 0.8175 (t80) REVERT: B 434 LYS cc_start: 0.6400 (tttt) cc_final: 0.6117 (ttpt) REVERT: B 457 LEU cc_start: 0.7341 (tp) cc_final: 0.7046 (tt) REVERT: B 540 ASP cc_start: 0.7878 (p0) cc_final: 0.7545 (m-30) REVERT: B 579 MET cc_start: 0.4549 (tmm) cc_final: 0.4023 (tmm) REVERT: B 698 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 644 VAL cc_start: 0.9236 (t) cc_final: 0.8992 (t) REVERT: C 677 MET cc_start: 0.6892 (tpp) cc_final: 0.6034 (ttp) REVERT: C 678 LEU cc_start: 0.8420 (mt) cc_final: 0.8158 (tt) REVERT: C 685 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7475 (mtm110) REVERT: D 449 CYS cc_start: 0.4142 (m) cc_final: 0.3905 (t) REVERT: D 462 MET cc_start: 0.7604 (mtp) cc_final: 0.7261 (mtt) REVERT: D 554 MET cc_start: 0.8198 (mmm) cc_final: 0.7979 (mmm) REVERT: D 696 ARG cc_start: 0.7368 (mtp180) cc_final: 0.6678 (tmt170) outliers start: 19 outliers final: 17 residues processed: 195 average time/residue: 0.6026 time to fit residues: 164.1607 Evaluate side-chains 194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 691 ASN C 578 HIS D 709 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.167319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.114943 restraints weight = 31256.497| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.99 r_work: 0.2956 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9776 Z= 0.109 Angle : 0.446 4.540 13288 Z= 0.245 Chirality : 0.037 0.145 1496 Planarity : 0.004 0.034 1620 Dihedral : 4.033 16.216 1280 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.27 % Allowed : 7.94 % Favored : 90.78 % 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: 2.00 (0.26), residues: 1140 helix: 1.55 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.80 (0.45), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.003 0.001 HIS C 703 PHE 0.015 0.001 PHE A 656 TYR 0.012 0.001 TYR C 611 ARG 0.004 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 667) hydrogen bonds : angle 4.04470 ( 1950) covalent geometry : bond 0.00226 ( 9776) covalent geometry : angle 0.44559 (13288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 MET cc_start: 0.8145 (tpp) cc_final: 0.7876 (tpt) REVERT: A 686 PHE cc_start: 0.8084 (t80) cc_final: 0.7769 (t80) REVERT: A 688 GLN cc_start: 0.8635 (mp10) cc_final: 0.8213 (mp10) REVERT: A 690 PRO cc_start: 0.8170 (Cg_exo) cc_final: 0.7905 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6361 (tttt) cc_final: 0.6080 (ttpt) REVERT: B 457 LEU cc_start: 0.7352 (tp) cc_final: 0.7038 (tt) REVERT: B 540 ASP cc_start: 0.7958 (p0) cc_final: 0.7534 (m-30) REVERT: B 576 GLN cc_start: 0.8529 (tm-30) cc_final: 0.7594 (tt0) REVERT: B 579 MET cc_start: 0.4639 (tmm) cc_final: 0.3939 (tmm) REVERT: B 695 GLN cc_start: 0.8120 (mt0) cc_final: 0.7380 (mp10) REVERT: C 677 MET cc_start: 0.6845 (tpp) cc_final: 0.6012 (ttp) REVERT: C 678 LEU cc_start: 0.8390 (mt) cc_final: 0.8162 (tt) REVERT: C 685 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7410 (mtm110) REVERT: D 462 MET cc_start: 0.7511 (mtp) cc_final: 0.7162 (mtt) REVERT: D 696 ARG cc_start: 0.7416 (mtp180) cc_final: 0.6771 (tmt170) outliers start: 13 outliers final: 10 residues processed: 190 average time/residue: 0.4875 time to fit residues: 129.1286 Evaluate side-chains 192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain C residue 578 HIS Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 ASN C 578 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.167204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.112260 restraints weight = 31365.988| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.12 r_work: 0.2900 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9776 Z= 0.123 Angle : 0.448 4.701 13288 Z= 0.245 Chirality : 0.037 0.146 1496 Planarity : 0.003 0.033 1620 Dihedral : 3.875 16.150 1280 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Rotamer: Outliers : 1.18 % Allowed : 8.43 % Favored : 90.39 % 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: 2.15 (0.26), residues: 1140 helix: 1.67 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.79 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.006 0.001 HIS C 578 PHE 0.017 0.001 PHE A 656 TYR 0.013 0.001 TYR C 611 ARG 0.002 0.000 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 667) hydrogen bonds : angle 3.93507 ( 1950) covalent geometry : bond 0.00265 ( 9776) covalent geometry : angle 0.44811 (13288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 MET cc_start: 0.8135 (tpp) cc_final: 0.7853 (tpt) REVERT: A 686 PHE cc_start: 0.8068 (t80) cc_final: 0.7749 (t80) REVERT: A 688 GLN cc_start: 0.8618 (mp10) cc_final: 0.8196 (mp10) REVERT: A 690 PRO cc_start: 0.8150 (Cg_exo) cc_final: 0.7880 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6320 (tttt) cc_final: 0.6047 (ttpt) REVERT: B 457 LEU cc_start: 0.7342 (tp) cc_final: 0.6980 (tt) REVERT: B 540 ASP cc_start: 0.7994 (p0) cc_final: 0.7532 (m-30) REVERT: B 576 GLN cc_start: 0.8578 (tm-30) cc_final: 0.7654 (tt0) REVERT: B 579 MET cc_start: 0.4367 (tmm) cc_final: 0.3627 (tmm) REVERT: C 677 MET cc_start: 0.6851 (tpp) cc_final: 0.6028 (ttp) REVERT: C 678 LEU cc_start: 0.8394 (mt) cc_final: 0.8169 (tt) REVERT: C 685 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7405 (mtm110) REVERT: D 462 MET cc_start: 0.7424 (mtp) cc_final: 0.7081 (mtt) REVERT: D 696 ARG cc_start: 0.7347 (mtp180) cc_final: 0.6731 (tmt170) outliers start: 12 outliers final: 8 residues processed: 190 average time/residue: 0.4807 time to fit residues: 125.5236 Evaluate side-chains 186 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain D residue 695 GLN Chi-restraints excluded: chain D residue 699 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 573 ASN C 578 HIS C 703 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.166828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.113302 restraints weight = 31288.307| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.21 r_work: 0.2959 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9776 Z= 0.133 Angle : 0.451 4.734 13288 Z= 0.247 Chirality : 0.037 0.147 1496 Planarity : 0.004 0.053 1620 Dihedral : 3.794 16.184 1280 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.37 % Allowed : 8.24 % Favored : 90.39 % 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: 2.40 (0.26), residues: 1140 helix: 1.80 (0.18), residues: 880 sheet: None (None), residues: 0 loop : 1.13 (0.46), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 568 HIS 0.007 0.001 HIS C 703 PHE 0.018 0.001 PHE A 656 TYR 0.017 0.001 TYR D 493 ARG 0.007 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 667) hydrogen bonds : angle 3.89288 ( 1950) covalent geometry : bond 0.00292 ( 9776) covalent geometry : angle 0.45124 (13288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.8025 (mttt) cc_final: 0.7107 (tptp) REVERT: A 677 MET cc_start: 0.8080 (tpp) cc_final: 0.7775 (tpt) REVERT: A 686 PHE cc_start: 0.8126 (t80) cc_final: 0.7846 (t80) REVERT: A 688 GLN cc_start: 0.8632 (mp10) cc_final: 0.8207 (mp10) REVERT: A 690 PRO cc_start: 0.8097 (Cg_exo) cc_final: 0.7818 (Cg_endo) REVERT: A 695 GLN cc_start: 0.8225 (mm-40) cc_final: 0.8007 (mm110) REVERT: B 434 LYS cc_start: 0.6272 (tttt) cc_final: 0.5976 (ttpt) REVERT: B 457 LEU cc_start: 0.7417 (tp) cc_final: 0.7020 (tt) REVERT: B 540 ASP cc_start: 0.7907 (p0) cc_final: 0.7472 (m-30) REVERT: B 576 GLN cc_start: 0.8591 (tm-30) cc_final: 0.7690 (tt0) REVERT: B 579 MET cc_start: 0.4527 (tmm) cc_final: 0.3798 (tmm) REVERT: B 681 ARG cc_start: 0.7134 (ttp-170) cc_final: 0.6933 (mtm180) REVERT: B 685 ARG cc_start: 0.8216 (mtm180) cc_final: 0.7769 (mtm-85) REVERT: C 677 MET cc_start: 0.6914 (tpp) cc_final: 0.6100 (ttp) REVERT: C 678 LEU cc_start: 0.8424 (mt) cc_final: 0.8201 (tt) REVERT: C 685 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7389 (mtm110) REVERT: C 695 GLN cc_start: 0.7267 (mp10) cc_final: 0.6904 (mp10) REVERT: D 462 MET cc_start: 0.7353 (mtp) cc_final: 0.7012 (mtt) REVERT: D 696 ARG cc_start: 0.7338 (mtp180) cc_final: 0.6736 (ttp-170) outliers start: 14 outliers final: 11 residues processed: 192 average time/residue: 0.4948 time to fit residues: 131.2312 Evaluate side-chains 189 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 695 GLN Chi-restraints excluded: chain D residue 699 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 74 optimal weight: 0.0770 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN C 578 HIS C 703 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.168165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3156 r_free = 0.3156 target = 0.112684 restraints weight = 31054.014| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.96 r_work: 0.2982 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9776 Z= 0.112 Angle : 0.438 4.810 13288 Z= 0.238 Chirality : 0.037 0.146 1496 Planarity : 0.003 0.039 1620 Dihedral : 3.716 16.135 1280 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.08 % Allowed : 8.53 % Favored : 90.39 % 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: 2.54 (0.26), residues: 1140 helix: 1.90 (0.18), residues: 880 sheet: None (None), residues: 0 loop : 1.19 (0.46), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.012 0.001 HIS C 703 PHE 0.017 0.001 PHE A 656 TYR 0.013 0.001 TYR D 493 ARG 0.006 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 667) hydrogen bonds : angle 3.82269 ( 1950) covalent geometry : bond 0.00239 ( 9776) covalent geometry : angle 0.43828 (13288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.8022 (mttt) cc_final: 0.7096 (tptp) REVERT: A 677 MET cc_start: 0.8091 (tpp) cc_final: 0.7826 (tpt) REVERT: A 688 GLN cc_start: 0.8554 (mp10) cc_final: 0.8148 (mp10) REVERT: A 690 PRO cc_start: 0.8087 (Cg_exo) cc_final: 0.7809 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6295 (tttt) cc_final: 0.5970 (ttpt) REVERT: B 457 LEU cc_start: 0.7392 (tp) cc_final: 0.6997 (tt) REVERT: B 540 ASP cc_start: 0.7919 (p0) cc_final: 0.7460 (m-30) REVERT: B 574 MET cc_start: 0.8121 (mtt) cc_final: 0.7811 (mtm) REVERT: B 576 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7476 (tt0) REVERT: B 579 MET cc_start: 0.4634 (tmm) cc_final: 0.3865 (tmm) REVERT: B 685 ARG cc_start: 0.8201 (mtm180) cc_final: 0.7757 (mtm-85) REVERT: C 677 MET cc_start: 0.6986 (tpp) cc_final: 0.6181 (ttp) REVERT: C 678 LEU cc_start: 0.8406 (mt) cc_final: 0.8196 (tt) REVERT: C 679 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7112 (tmt170) REVERT: C 685 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7379 (mtm110) REVERT: C 695 GLN cc_start: 0.7283 (mp10) cc_final: 0.6922 (mp10) REVERT: D 462 MET cc_start: 0.7295 (mtp) cc_final: 0.6953 (mtt) REVERT: D 696 ARG cc_start: 0.7200 (mtp180) cc_final: 0.6638 (ttp-170) outliers start: 11 outliers final: 8 residues processed: 187 average time/residue: 0.4817 time to fit residues: 125.2509 Evaluate side-chains 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 573 ASN C 578 HIS C 635 ASN C 703 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.167193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.111532 restraints weight = 31438.923| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.19 r_work: 0.2875 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9776 Z= 0.147 Angle : 0.460 5.292 13288 Z= 0.251 Chirality : 0.038 0.147 1496 Planarity : 0.004 0.037 1620 Dihedral : 3.721 16.138 1280 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.27 % Allowed : 8.73 % Favored : 90.00 % 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: 2.45 (0.26), residues: 1140 helix: 1.84 (0.17), residues: 880 sheet: None (None), residues: 0 loop : 1.11 (0.46), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 568 HIS 0.011 0.001 HIS C 703 PHE 0.018 0.001 PHE A 656 TYR 0.013 0.001 TYR D 493 ARG 0.005 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 667) hydrogen bonds : angle 3.85710 ( 1950) covalent geometry : bond 0.00329 ( 9776) covalent geometry : angle 0.46013 (13288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.8056 (mttt) cc_final: 0.7151 (tptp) REVERT: A 677 MET cc_start: 0.8210 (tpp) cc_final: 0.7885 (tpt) REVERT: A 688 GLN cc_start: 0.8579 (mp10) cc_final: 0.8177 (mp10) REVERT: A 690 PRO cc_start: 0.8268 (Cg_exo) cc_final: 0.7985 (Cg_endo) REVERT: A 701 PHE cc_start: 0.8592 (t80) cc_final: 0.8309 (t80) REVERT: B 434 LYS cc_start: 0.6375 (tttt) cc_final: 0.6040 (ttpt) REVERT: B 457 LEU cc_start: 0.7501 (tp) cc_final: 0.7081 (tt) REVERT: B 540 ASP cc_start: 0.8055 (p0) cc_final: 0.7557 (m-30) REVERT: B 576 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7753 (tt0) REVERT: B 579 MET cc_start: 0.4701 (tmm) cc_final: 0.3926 (tmm) REVERT: B 685 ARG cc_start: 0.8219 (mtm180) cc_final: 0.7738 (mtm-85) REVERT: C 677 MET cc_start: 0.7145 (tpp) cc_final: 0.6322 (ttp) REVERT: C 678 LEU cc_start: 0.8402 (mt) cc_final: 0.8201 (tt) REVERT: C 679 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.7237 (tmt170) REVERT: C 685 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7487 (mtm110) REVERT: C 695 GLN cc_start: 0.7507 (mp10) cc_final: 0.7109 (mp10) REVERT: C 699 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7219 (mt-10) REVERT: D 462 MET cc_start: 0.7607 (mtp) cc_final: 0.7283 (mtt) REVERT: D 696 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6840 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 181 average time/residue: 0.6973 time to fit residues: 179.2205 Evaluate side-chains 182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 695 GLN B 573 ASN C 578 HIS C 635 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.168490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.111834 restraints weight = 31177.490| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.01 r_work: 0.2926 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9776 Z= 0.113 Angle : 0.438 6.026 13288 Z= 0.237 Chirality : 0.037 0.145 1496 Planarity : 0.003 0.033 1620 Dihedral : 3.643 16.150 1280 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.47 % Allowed : 8.24 % Favored : 90.29 % 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: 2.56 (0.26), residues: 1140 helix: 1.94 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 1.07 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.017 0.001 HIS C 703 PHE 0.017 0.001 PHE A 656 TYR 0.012 0.001 TYR C 611 ARG 0.005 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 667) hydrogen bonds : angle 3.76289 ( 1950) covalent geometry : bond 0.00243 ( 9776) covalent geometry : angle 0.43789 (13288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 PHE cc_start: 0.7794 (m-80) cc_final: 0.7546 (m-80) REVERT: A 495 LYS cc_start: 0.8039 (mttt) cc_final: 0.7142 (tptp) REVERT: A 677 MET cc_start: 0.8144 (tpp) cc_final: 0.7875 (tpt) REVERT: A 688 GLN cc_start: 0.8547 (mp10) cc_final: 0.8128 (mp10) REVERT: A 690 PRO cc_start: 0.8148 (Cg_exo) cc_final: 0.7870 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6286 (tttt) cc_final: 0.6019 (ttpt) REVERT: B 457 LEU cc_start: 0.7405 (tp) cc_final: 0.6994 (tt) REVERT: B 540 ASP cc_start: 0.7979 (p0) cc_final: 0.7474 (m-30) REVERT: B 576 GLN cc_start: 0.8600 (tm-30) cc_final: 0.7675 (tt0) REVERT: B 579 MET cc_start: 0.4742 (tmm) cc_final: 0.3948 (tmm) REVERT: B 685 ARG cc_start: 0.8201 (mtm180) cc_final: 0.7724 (mtm-85) REVERT: C 652 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: C 677 MET cc_start: 0.7045 (tpp) cc_final: 0.6226 (ttp) REVERT: C 679 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7223 (tmt170) REVERT: C 685 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7443 (mtm110) REVERT: C 695 GLN cc_start: 0.7299 (mp10) cc_final: 0.6851 (mp10) REVERT: D 462 MET cc_start: 0.7374 (mtp) cc_final: 0.7032 (mtt) REVERT: D 696 ARG cc_start: 0.7262 (mtp180) cc_final: 0.6747 (ttp-170) outliers start: 15 outliers final: 11 residues processed: 187 average time/residue: 0.4943 time to fit residues: 128.7791 Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 573 ASN C 578 HIS C 703 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.167894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.112619 restraints weight = 31279.561| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.99 r_work: 0.2917 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9776 Z= 0.118 Angle : 0.437 5.312 13288 Z= 0.237 Chirality : 0.037 0.145 1496 Planarity : 0.003 0.033 1620 Dihedral : 3.608 16.083 1280 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.18 % Allowed : 9.02 % Favored : 89.80 % 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: 2.64 (0.26), residues: 1140 helix: 2.00 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 1.09 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.006 0.001 HIS C 703 PHE 0.018 0.001 PHE A 656 TYR 0.012 0.001 TYR C 611 ARG 0.005 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 667) hydrogen bonds : angle 3.74250 ( 1950) covalent geometry : bond 0.00258 ( 9776) covalent geometry : angle 0.43744 (13288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 PHE cc_start: 0.7854 (m-80) cc_final: 0.7612 (m-80) REVERT: A 495 LYS cc_start: 0.8073 (mttt) cc_final: 0.7346 (ptmm) REVERT: A 677 MET cc_start: 0.8157 (tpp) cc_final: 0.7884 (tpt) REVERT: A 688 GLN cc_start: 0.8638 (mp10) cc_final: 0.8200 (mp10) REVERT: A 690 PRO cc_start: 0.8146 (Cg_exo) cc_final: 0.7833 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6204 (tttt) cc_final: 0.5954 (ttpt) REVERT: B 457 LEU cc_start: 0.7372 (tp) cc_final: 0.7005 (tt) REVERT: B 540 ASP cc_start: 0.8043 (p0) cc_final: 0.7513 (m-30) REVERT: B 576 GLN cc_start: 0.8631 (tm-30) cc_final: 0.7716 (tt0) REVERT: B 579 MET cc_start: 0.4802 (tmm) cc_final: 0.3990 (tmm) REVERT: C 652 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: C 677 MET cc_start: 0.7077 (tpp) cc_final: 0.6242 (ttp) REVERT: C 679 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7276 (tmt170) REVERT: C 685 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7497 (mtm110) REVERT: C 695 GLN cc_start: 0.7520 (mp10) cc_final: 0.7093 (mp10) REVERT: D 462 MET cc_start: 0.7514 (mtp) cc_final: 0.7179 (mtt) REVERT: D 470 ASN cc_start: 0.7706 (m-40) cc_final: 0.7248 (m-40) REVERT: D 696 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6788 (ttp-170) outliers start: 12 outliers final: 10 residues processed: 182 average time/residue: 0.4984 time to fit residues: 125.5270 Evaluate side-chains 186 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 695 GLN C 578 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.167611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.112254 restraints weight = 31282.813| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.94 r_work: 0.2930 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9776 Z= 0.134 Angle : 0.452 6.389 13288 Z= 0.245 Chirality : 0.037 0.146 1496 Planarity : 0.003 0.032 1620 Dihedral : 3.614 16.112 1280 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.27 % Allowed : 9.41 % Favored : 89.31 % 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: 2.58 (0.26), residues: 1140 helix: 1.95 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 1.06 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 568 HIS 0.013 0.001 HIS C 703 PHE 0.018 0.001 PHE C 463 TYR 0.012 0.001 TYR C 611 ARG 0.004 0.000 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 667) hydrogen bonds : angle 3.77374 ( 1950) covalent geometry : bond 0.00298 ( 9776) covalent geometry : angle 0.45215 (13288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11740.05 seconds wall clock time: 204 minutes 57.83 seconds (12297.83 seconds total)