Starting phenix.real_space_refine on Sun Aug 24 10:11:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chs_45600/08_2025/9chs_45600.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chs_45600/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9chs_45600/08_2025/9chs_45600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chs_45600/08_2025/9chs_45600.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9chs_45600/08_2025/9chs_45600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chs_45600/08_2025/9chs_45600.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.97, per 1000 atoms: 0.21 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: 1.39 Conformation dependent library (CDL) restraints added in 653.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.38 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: 4.49 Time building geometry restraints manager: 2.05 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: 0.01 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.540 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG C 681 TYR 0.135 0.024 TYR A 545 PHE 0.075 0.011 PHE C 701 TRP 0.091 0.014 TRP B 585 HIS 0.010 0.002 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.01283 ( 9776) covalent geometry : angle 1.70141 (13288) hydrogen bonds : bond 0.16580 ( 667) hydrogen bonds : angle 7.03064 ( 1950) *********************** 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 : 0.506 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: A 651 MET cc_start: 0.7732 (mmm) cc_final: 0.7419 (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: 0.7708 (tpp) REVERT: A 690 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.8026 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7534 (tp) cc_final: 0.7222 (tt) REVERT: B 540 ASP cc_start: 0.8003 (p0) cc_final: 0.7639 (m-30) REVERT: C 673 TYR cc_start: 0.7713 (t80) cc_final: 0.7371 (t80) REVERT: C 677 MET cc_start: 0.6611 (tpp) cc_final: 0.5939 (ttp) REVERT: C 678 LEU cc_start: 0.8280 (mt) cc_final: 0.7976 (tt) REVERT: C 694 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7195 (ttt180) REVERT: D 462 MET cc_start: 0.7537 (mtp) cc_final: 0.7150 (mtp) REVERT: D 488 ARG cc_start: 0.6215 (mpt180) cc_final: 0.6010 (mpt180) REVERT: D 691 ASN cc_start: 0.8232 (t0) cc_final: 0.8019 (t0) REVERT: D 696 ARG cc_start: 0.7274 (mtp180) cc_final: 0.6698 (tmt170) REVERT: D 699 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7221 (mt-10) REVERT: D 703 HIS cc_start: 0.7967 (t-90) cc_final: 0.7709 (t70) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.2949 time to fit residues: 96.8447 Evaluate side-chains 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 691 ASN D 687 HIS ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.167447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.111003 restraints weight = 31508.700| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.29 r_work: 0.2891 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9776 Z= 0.156 Angle : 0.559 4.938 13288 Z= 0.313 Chirality : 0.040 0.143 1496 Planarity : 0.004 0.038 1620 Dihedral : 4.602 18.418 1280 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.37 % Allowed : 4.51 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1140 helix: 0.95 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.61 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 528 TYR 0.015 0.002 TYR B 611 PHE 0.015 0.002 PHE B 701 TRP 0.013 0.001 TRP A 568 HIS 0.004 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9776) covalent geometry : angle 0.55905 (13288) hydrogen bonds : bond 0.05020 ( 667) hydrogen bonds : angle 4.45279 ( 1950) *********************** 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 227 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.538 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: A 452 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6117 (tp) REVERT: A 574 MET cc_start: 0.8614 (mtt) cc_final: 0.8365 (mtp) REVERT: A 651 MET cc_start: 0.7443 (mmm) cc_final: 0.6835 (ppp) REVERT: A 677 MET cc_start: 0.8059 (tpp) cc_final: 0.7743 (tpt) REVERT: A 679 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.7037 (ttm-80) REVERT: A 690 PRO cc_start: 0.7814 (Cg_exo) cc_final: 0.7568 (Cg_endo) REVERT: A 698 GLU cc_start: 0.8396 (pt0) cc_final: 0.8171 (pt0) REVERT: B 457 LEU cc_start: 0.7303 (tp) cc_final: 0.6997 (tt) REVERT: B 540 ASP cc_start: 0.7924 (p0) cc_final: 0.7617 (m-30) REVERT: B 550 LEU cc_start: 0.8285 (mt) cc_final: 0.8081 (tt) REVERT: C 644 VAL cc_start: 0.9125 (t) cc_final: 0.8876 (t) REVERT: C 673 TYR cc_start: 0.7496 (t80) cc_final: 0.7269 (t80) REVERT: C 677 MET cc_start: 0.6709 (tpp) cc_final: 0.5858 (ttp) REVERT: C 678 LEU cc_start: 0.8438 (mt) cc_final: 0.8077 (tt) REVERT: C 679 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8012 (mtp85) REVERT: C 685 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7528 (mtp85) REVERT: D 449 CYS cc_start: 0.4340 (m) cc_final: 0.3994 (t) REVERT: D 462 MET cc_start: 0.7496 (mtp) cc_final: 0.7182 (mtt) REVERT: D 554 MET cc_start: 0.8192 (mmm) cc_final: 0.7985 (mmm) REVERT: D 663 ILE cc_start: 0.7456 (mm) cc_final: 0.7224 (pt) REVERT: D 696 ARG cc_start: 0.7451 (mtp180) cc_final: 0.6696 (tmt170) REVERT: D 699 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7106 (mt-10) outliers start: 14 outliers final: 12 residues processed: 223 average time/residue: 0.2320 time to fit residues: 70.9410 Evaluate side-chains 206 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 81 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 709 ASN D 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.164512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.108194 restraints weight = 31652.600| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.03 r_work: 0.2876 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9776 Z= 0.192 Angle : 0.526 5.122 13288 Z= 0.293 Chirality : 0.040 0.151 1496 Planarity : 0.004 0.039 1620 Dihedral : 4.269 17.075 1280 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.47 % Allowed : 6.86 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.25), residues: 1140 helix: 1.23 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.65 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.014 0.002 TYR B 611 PHE 0.016 0.001 PHE A 656 TRP 0.015 0.001 TRP A 568 HIS 0.005 0.001 HIS D 578 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9776) covalent geometry : angle 0.52608 (13288) hydrogen bonds : bond 0.04553 ( 667) hydrogen bonds : angle 4.28745 ( 1950) *********************** 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: 15 poor density : 190 time to evaluate : 0.512 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: 0.8125 (tpp) cc_final: 0.7810 (tpt) REVERT: A 688 GLN cc_start: 0.8627 (mp10) cc_final: 0.8145 (mp10) REVERT: A 690 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7891 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6250 (tttt) cc_final: 0.5990 (ttpt) REVERT: B 457 LEU cc_start: 0.7295 (tp) cc_final: 0.6968 (tt) REVERT: B 540 ASP cc_start: 0.7838 (p0) cc_final: 0.7530 (m-30) REVERT: B 576 GLN cc_start: 0.8477 (tm-30) cc_final: 0.7495 (tt0) REVERT: B 579 MET cc_start: 0.4494 (tmm) cc_final: 0.3963 (tmm) REVERT: C 554 MET cc_start: 0.7798 (mmp) cc_final: 0.7406 (mmp) REVERT: C 644 VAL cc_start: 0.9201 (t) cc_final: 0.8954 (t) REVERT: C 673 TYR cc_start: 0.7657 (t80) cc_final: 0.7436 (t80) REVERT: C 677 MET cc_start: 0.6885 (tpp) cc_final: 0.6043 (ttp) REVERT: C 678 LEU cc_start: 0.8403 (mt) cc_final: 0.8149 (tt) REVERT: C 685 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7451 (mtm110) REVERT: D 449 CYS cc_start: 0.4006 (m) cc_final: 0.3732 (t) REVERT: D 462 MET cc_start: 0.7574 (mtp) cc_final: 0.7235 (mtt) REVERT: D 554 MET cc_start: 0.8196 (mmm) cc_final: 0.7972 (mmm) REVERT: D 696 ARG cc_start: 0.7271 (mtp180) cc_final: 0.6703 (tmt170) outliers start: 15 outliers final: 14 residues processed: 196 average time/residue: 0.2261 time to fit residues: 61.2054 Evaluate side-chains 194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 550 LEU 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 573 ASN Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 467 ILE 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 48 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 691 ASN B 709 ASN C 578 HIS D 709 ASN 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 = 0.167123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3142 r_free = 0.3142 target = 0.111999 restraints weight = 31366.875| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.04 r_work: 0.2894 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9776 Z= 0.119 Angle : 0.451 4.460 13288 Z= 0.248 Chirality : 0.037 0.145 1496 Planarity : 0.004 0.034 1620 Dihedral : 4.014 16.328 1280 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.37 % Allowed : 7.45 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.26), residues: 1140 helix: 1.54 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.74 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 528 TYR 0.013 0.001 TYR D 493 PHE 0.015 0.001 PHE A 656 TRP 0.012 0.001 TRP A 568 HIS 0.003 0.001 HIS C 703 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9776) covalent geometry : angle 0.45053 (13288) hydrogen bonds : bond 0.03982 ( 667) hydrogen bonds : angle 4.02826 ( 1950) *********************** 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 202 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.514 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: A 677 MET cc_start: 0.8175 (tpp) cc_final: 0.7910 (tpt) REVERT: A 688 GLN cc_start: 0.8642 (mp10) cc_final: 0.8209 (mp10) REVERT: A 690 PRO cc_start: 0.8234 (Cg_exo) cc_final: 0.7971 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6448 (tttt) cc_final: 0.6148 (ttpt) REVERT: B 457 LEU cc_start: 0.7462 (tp) cc_final: 0.7074 (tt) REVERT: B 540 ASP cc_start: 0.8012 (p0) cc_final: 0.7585 (m-30) REVERT: B 576 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7573 (tt0) REVERT: B 579 MET cc_start: 0.4620 (tmm) cc_final: 0.3922 (tmm) REVERT: B 695 GLN cc_start: 0.8203 (mt0) cc_final: 0.7424 (mp10) REVERT: C 673 TYR cc_start: 0.7667 (t80) cc_final: 0.7438 (t80) REVERT: C 677 MET cc_start: 0.6968 (tpp) cc_final: 0.6085 (ttp) REVERT: C 678 LEU cc_start: 0.8383 (mt) cc_final: 0.8164 (tt) REVERT: C 685 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7462 (mtm110) REVERT: D 462 MET cc_start: 0.7669 (mtp) cc_final: 0.7324 (mtt) REVERT: D 696 ARG cc_start: 0.7425 (mtp180) cc_final: 0.6843 (ttp-170) outliers start: 14 outliers final: 11 residues processed: 194 average time/residue: 0.2307 time to fit residues: 61.9154 Evaluate side-chains 192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 550 LEU 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 620 SER 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 102 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.165642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.112294 restraints weight = 31372.086| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.97 r_work: 0.2890 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9776 Z= 0.168 Angle : 0.481 4.587 13288 Z= 0.266 Chirality : 0.038 0.149 1496 Planarity : 0.004 0.038 1620 Dihedral : 3.942 17.106 1280 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.47 % Allowed : 7.84 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.26), residues: 1140 helix: 1.58 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 0.97 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.014 0.002 TYR B 611 PHE 0.018 0.001 PHE A 656 TRP 0.013 0.001 TRP A 568 HIS 0.004 0.001 HIS D 578 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9776) covalent geometry : angle 0.48108 (13288) hydrogen bonds : bond 0.04100 ( 667) hydrogen bonds : angle 4.04097 ( 1950) *********************** 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: 15 poor density : 181 time to evaluate : 0.488 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: A 495 LYS cc_start: 0.7991 (mttt) cc_final: 0.7139 (tptp) REVERT: A 677 MET cc_start: 0.8172 (tpp) cc_final: 0.7870 (tpt) REVERT: A 686 PHE cc_start: 0.8091 (t80) cc_final: 0.7767 (t80) REVERT: A 688 GLN cc_start: 0.8642 (mp10) cc_final: 0.8220 (mp10) REVERT: A 690 PRO cc_start: 0.8230 (Cg_exo) cc_final: 0.7944 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6259 (tttt) cc_final: 0.6029 (ttpt) REVERT: B 457 LEU cc_start: 0.7411 (tp) cc_final: 0.7041 (tt) REVERT: B 540 ASP cc_start: 0.8041 (p0) cc_final: 0.7578 (m-30) REVERT: B 576 GLN cc_start: 0.8530 (tm-30) cc_final: 0.7702 (tt0) REVERT: B 579 MET cc_start: 0.4507 (tmm) cc_final: 0.3786 (tmm) REVERT: C 644 VAL cc_start: 0.9179 (t) cc_final: 0.8927 (t) REVERT: C 673 TYR cc_start: 0.7660 (t80) cc_final: 0.7390 (t80) REVERT: C 677 MET cc_start: 0.7034 (tpp) cc_final: 0.6167 (ttp) REVERT: C 678 LEU cc_start: 0.8387 (mt) cc_final: 0.8172 (tt) REVERT: C 685 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7443 (mtm110) REVERT: D 462 MET cc_start: 0.7552 (mtp) cc_final: 0.7198 (mtt) REVERT: D 696 ARG cc_start: 0.7370 (mtp180) cc_final: 0.6810 (ttp-170) outliers start: 15 outliers final: 8 residues processed: 187 average time/residue: 0.2359 time to fit residues: 60.6619 Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 578 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.165909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.111479 restraints weight = 31049.893| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.96 r_work: 0.2894 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9776 Z= 0.149 Angle : 0.460 4.517 13288 Z= 0.253 Chirality : 0.038 0.147 1496 Planarity : 0.004 0.036 1620 Dihedral : 3.861 16.911 1280 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.57 % Allowed : 8.33 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.26), residues: 1140 helix: 1.64 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.96 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.014 0.001 TYR D 493 PHE 0.018 0.001 PHE A 656 TRP 0.013 0.001 TRP A 568 HIS 0.003 0.001 HIS D 578 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9776) covalent geometry : angle 0.45992 (13288) hydrogen bonds : bond 0.03894 ( 667) hydrogen bonds : angle 3.96896 ( 1950) *********************** 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 201 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.500 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: 0.8024 (mttt) cc_final: 0.7129 (tptp) REVERT: A 677 MET cc_start: 0.8135 (tpp) cc_final: 0.7819 (tpt) REVERT: A 688 GLN cc_start: 0.8616 (mp10) cc_final: 0.8205 (mp10) REVERT: A 690 PRO cc_start: 0.8188 (Cg_exo) cc_final: 0.7898 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6311 (tttt) cc_final: 0.6062 (ttpt) REVERT: B 457 LEU cc_start: 0.7452 (tp) cc_final: 0.7044 (tt) REVERT: B 540 ASP cc_start: 0.8022 (p0) cc_final: 0.7523 (m-30) REVERT: B 576 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7715 (tt0) REVERT: B 579 MET cc_start: 0.4711 (tmm) cc_final: 0.3959 (tmm) REVERT: B 685 ARG cc_start: 0.8246 (mtp180) cc_final: 0.8004 (mtp85) REVERT: B 695 GLN cc_start: 0.8039 (mt0) cc_final: 0.7306 (mp10) REVERT: C 644 VAL cc_start: 0.9143 (t) cc_final: 0.8903 (t) REVERT: C 673 TYR cc_start: 0.7634 (t80) cc_final: 0.7338 (t80) REVERT: C 677 MET cc_start: 0.7057 (tpp) cc_final: 0.6176 (ttp) REVERT: C 678 LEU cc_start: 0.8387 (mt) cc_final: 0.8171 (tt) REVERT: C 679 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.7237 (tmt170) REVERT: C 685 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7450 (mtm110) REVERT: D 462 MET cc_start: 0.7544 (mtp) cc_final: 0.7177 (mtt) REVERT: D 578 HIS cc_start: 0.6509 (t-90) cc_final: 0.5770 (m170) REVERT: D 696 ARG cc_start: 0.7341 (mtp180) cc_final: 0.6763 (ttp-170) outliers start: 16 outliers final: 13 residues processed: 193 average time/residue: 0.2403 time to fit residues: 63.8559 Evaluate side-chains 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 602 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 578 HIS Chi-restraints excluded: chain C residue 620 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN C 703 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.165056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.111554 restraints weight = 31272.691| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.20 r_work: 0.2886 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9776 Z= 0.179 Angle : 0.482 4.578 13288 Z= 0.266 Chirality : 0.038 0.148 1496 Planarity : 0.004 0.038 1620 Dihedral : 3.873 17.219 1280 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.27 % Allowed : 8.63 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.26), residues: 1140 helix: 1.57 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.88 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.014 0.002 TYR B 611 PHE 0.019 0.001 PHE B 656 TRP 0.014 0.001 TRP D 568 HIS 0.007 0.001 HIS C 703 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9776) covalent geometry : angle 0.48219 (13288) hydrogen bonds : bond 0.04017 ( 667) hydrogen bonds : angle 4.01820 ( 1950) *********************** 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 188 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.526 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: 0.8080 (mttt) cc_final: 0.7302 (ptmm) REVERT: A 677 MET cc_start: 0.8124 (tpp) cc_final: 0.7790 (tpt) REVERT: A 688 GLN cc_start: 0.8602 (mp10) cc_final: 0.8176 (mp10) REVERT: A 690 PRO cc_start: 0.8240 (Cg_exo) cc_final: 0.7960 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6352 (tttt) cc_final: 0.6087 (ttpt) REVERT: B 457 LEU cc_start: 0.7391 (tp) cc_final: 0.7012 (tt) REVERT: B 540 ASP cc_start: 0.8025 (p0) cc_final: 0.7529 (m-30) REVERT: B 576 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7569 (tt0) REVERT: B 579 MET cc_start: 0.4787 (tmm) cc_final: 0.3999 (tmm) REVERT: B 685 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7971 (mtp85) REVERT: C 644 VAL cc_start: 0.9145 (t) cc_final: 0.8897 (t) REVERT: C 673 TYR cc_start: 0.7642 (t80) cc_final: 0.7326 (t80) REVERT: C 677 MET cc_start: 0.7154 (tpp) cc_final: 0.6281 (ttp) REVERT: C 678 LEU cc_start: 0.8385 (mt) cc_final: 0.8164 (tt) REVERT: C 679 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.7244 (tmt170) REVERT: C 685 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7439 (mtm110) REVERT: D 462 MET cc_start: 0.7523 (mtp) cc_final: 0.7157 (mtt) REVERT: D 578 HIS cc_start: 0.6537 (t-90) cc_final: 0.5778 (m170) REVERT: D 696 ARG cc_start: 0.7292 (mtp180) cc_final: 0.6733 (ttp-170) outliers start: 13 outliers final: 13 residues processed: 182 average time/residue: 0.2492 time to fit residues: 61.8628 Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 578 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C 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 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 60 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 105 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.167056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.111068 restraints weight = 31270.308| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.00 r_work: 0.2919 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9776 Z= 0.112 Angle : 0.436 4.408 13288 Z= 0.239 Chirality : 0.037 0.145 1496 Planarity : 0.003 0.036 1620 Dihedral : 3.750 16.280 1280 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.27 % Allowed : 9.12 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.26), residues: 1140 helix: 1.77 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 0.93 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 534 TYR 0.016 0.001 TYR D 493 PHE 0.017 0.001 PHE A 656 TRP 0.012 0.001 TRP A 568 HIS 0.015 0.001 HIS C 703 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9776) covalent geometry : angle 0.43648 (13288) hydrogen bonds : bond 0.03733 ( 667) hydrogen bonds : angle 3.86411 ( 1950) *********************** 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 : 0.513 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: 0.8064 (mttt) cc_final: 0.7149 (tptp) REVERT: A 677 MET cc_start: 0.8151 (tpp) cc_final: 0.7872 (tpt) REVERT: A 688 GLN cc_start: 0.8557 (mp10) cc_final: 0.8141 (mp10) REVERT: A 690 PRO cc_start: 0.8157 (Cg_exo) cc_final: 0.7869 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6322 (tttt) cc_final: 0.6047 (ttpt) REVERT: B 457 LEU cc_start: 0.7450 (tp) cc_final: 0.7045 (tt) REVERT: B 540 ASP cc_start: 0.7978 (p0) cc_final: 0.7488 (m-30) REVERT: B 576 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7658 (tt0) REVERT: B 579 MET cc_start: 0.4823 (tmm) cc_final: 0.4018 (tmm) REVERT: B 681 ARG cc_start: 0.7046 (ttp-170) cc_final: 0.6768 (mtm180) REVERT: B 685 ARG cc_start: 0.8200 (mtp180) cc_final: 0.7956 (mtp85) REVERT: C 652 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: C 673 TYR cc_start: 0.7626 (t80) cc_final: 0.7301 (t80) REVERT: C 677 MET cc_start: 0.7149 (tpp) cc_final: 0.6282 (ttp) REVERT: C 685 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7427 (mtm110) REVERT: D 462 MET cc_start: 0.7436 (mtp) cc_final: 0.7091 (mtt) REVERT: D 578 HIS cc_start: 0.6763 (t-90) cc_final: 0.5841 (m170) REVERT: D 696 ARG cc_start: 0.7262 (mtp180) cc_final: 0.6718 (ttp-170) outliers start: 13 outliers final: 9 residues processed: 181 average time/residue: 0.2445 time to fit residues: 60.5138 Evaluate side-chains 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 703 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.164988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.111093 restraints weight = 31127.259| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.29 r_work: 0.2865 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9776 Z= 0.192 Angle : 0.498 5.103 13288 Z= 0.275 Chirality : 0.039 0.149 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.853 17.411 1280 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.18 % Allowed : 9.31 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.26), residues: 1140 helix: 1.62 (0.17), residues: 880 sheet: None (None), residues: 0 loop : 0.90 (0.46), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.015 0.002 TYR D 493 PHE 0.021 0.002 PHE B 656 TRP 0.013 0.001 TRP D 568 HIS 0.004 0.001 HIS C 703 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9776) covalent geometry : angle 0.49845 (13288) hydrogen bonds : bond 0.04066 ( 667) hydrogen bonds : angle 4.01144 ( 1950) *********************** 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 189 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.537 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: A 495 LYS cc_start: 0.8091 (mttt) cc_final: 0.7177 (tptp) REVERT: A 677 MET cc_start: 0.8258 (tpp) cc_final: 0.7986 (tpt) REVERT: A 688 GLN cc_start: 0.8694 (mp10) cc_final: 0.8236 (mp10) REVERT: B 434 LYS cc_start: 0.6377 (tttt) cc_final: 0.6132 (ttpt) REVERT: B 457 LEU cc_start: 0.7423 (tp) cc_final: 0.7027 (tt) REVERT: B 475 TYR cc_start: 0.7648 (p90) cc_final: 0.7414 (p90) REVERT: B 540 ASP cc_start: 0.8053 (p0) cc_final: 0.7584 (m-30) REVERT: B 576 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7792 (tt0) REVERT: B 579 MET cc_start: 0.4888 (tmm) cc_final: 0.4019 (tmm) REVERT: B 685 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7984 (mtp85) REVERT: C 644 VAL cc_start: 0.9206 (t) cc_final: 0.8961 (t) REVERT: C 652 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: C 673 TYR cc_start: 0.7687 (t80) cc_final: 0.7356 (t80) REVERT: C 677 MET cc_start: 0.7183 (tpp) cc_final: 0.6297 (ttp) REVERT: C 685 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7487 (mtm110) REVERT: D 462 MET cc_start: 0.7655 (mtp) cc_final: 0.7308 (mtt) REVERT: D 578 HIS cc_start: 0.6859 (t-90) cc_final: 0.5868 (m170) REVERT: D 696 ARG cc_start: 0.7361 (mtp180) cc_final: 0.6827 (ttp-170) outliers start: 12 outliers final: 10 residues processed: 183 average time/residue: 0.2399 time to fit residues: 60.2766 Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 C residue 578 HIS 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 97 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.167793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.116467 restraints weight = 31079.937| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.20 r_work: 0.2915 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4660 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= 0.100 Angle : 0.432 4.621 13288 Z= 0.236 Chirality : 0.037 0.143 1496 Planarity : 0.003 0.035 1620 Dihedral : 3.700 16.147 1280 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.18 % Allowed : 9.41 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.26), residues: 1140 helix: 1.85 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 0.97 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 534 TYR 0.012 0.001 TYR D 493 PHE 0.017 0.001 PHE A 656 TRP 0.013 0.001 TRP A 568 HIS 0.013 0.001 HIS C 703 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9776) covalent geometry : angle 0.43157 (13288) hydrogen bonds : bond 0.03651 ( 667) hydrogen bonds : angle 3.80873 ( 1950) ********************** 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 : 0.482 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: A 495 LYS cc_start: 0.8031 (mttt) cc_final: 0.7285 (ptmm) REVERT: A 677 MET cc_start: 0.8171 (tpp) cc_final: 0.7964 (tpt) REVERT: A 688 GLN cc_start: 0.8675 (mp10) cc_final: 0.8238 (mp10) REVERT: A 690 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7858 (Cg_endo) REVERT: B 434 LYS cc_start: 0.6344 (tttt) cc_final: 0.6072 (ttpt) REVERT: B 457 LEU cc_start: 0.7369 (tp) cc_final: 0.6993 (tt) REVERT: B 540 ASP cc_start: 0.7993 (p0) cc_final: 0.7482 (m-30) REVERT: B 576 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7635 (tt0) REVERT: B 579 MET cc_start: 0.4837 (tmm) cc_final: 0.3966 (tmm) REVERT: B 681 ARG cc_start: 0.6992 (ttp-170) cc_final: 0.6686 (mtm180) REVERT: B 685 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7963 (mtp85) REVERT: C 652 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: C 673 TYR cc_start: 0.7577 (t80) cc_final: 0.7242 (t80) REVERT: C 677 MET cc_start: 0.7098 (tpp) cc_final: 0.6224 (ttp) REVERT: C 685 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7441 (mtm110) REVERT: D 462 MET cc_start: 0.7383 (mtp) cc_final: 0.7025 (mtt) REVERT: D 578 HIS cc_start: 0.6778 (t-90) cc_final: 0.5788 (m170) REVERT: D 696 ARG cc_start: 0.7256 (mtp180) cc_final: 0.6685 (ttp-170) REVERT: D 698 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7893 (mm-30) outliers start: 12 outliers final: 10 residues processed: 183 average time/residue: 0.2302 time to fit residues: 57.8737 Evaluate side-chains 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 578 HIS Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 652 TYR 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 23 optimal weight: 0.0770 chunk 111 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 703 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.166276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.112474 restraints weight = 31413.468| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.29 r_work: 0.2878 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9776 Z= 0.165 Angle : 0.476 5.073 13288 Z= 0.261 Chirality : 0.038 0.148 1496 Planarity : 0.004 0.036 1620 Dihedral : 3.747 16.908 1280 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.47 % Allowed : 9.31 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.26), residues: 1140 helix: 1.73 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.93 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 528 TYR 0.014 0.002 TYR B 611 PHE 0.020 0.001 PHE B 656 TRP 0.013 0.001 TRP D 568 HIS 0.008 0.001 HIS C 703 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9776) covalent geometry : angle 0.47559 (13288) hydrogen bonds : bond 0.03872 ( 667) hydrogen bonds : angle 3.91399 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5486.27 seconds wall clock time: 93 minutes 56.81 seconds (5636.81 seconds total)