Starting phenix.real_space_refine on Wed Sep 17 16:02:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymp_39402/09_2025/8ymp_39402_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymp_39402/09_2025/8ymp_39402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ymp_39402/09_2025/8ymp_39402_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymp_39402/09_2025/8ymp_39402_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ymp_39402/09_2025/8ymp_39402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymp_39402/09_2025/8ymp_39402.map" } resolution = 2.6 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= 0.012 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6316 2.51 5 N 1560 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9570 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4776 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 32, 'TRANS': 559} Chain breaks: 3 Chain: "B" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4776 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 32, 'TRANS': 559} Chain breaks: 3 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.75, per 1000 atoms: 0.29 Number of scatterers: 9570 At special positions: 0 Unit cell: (149.91, 90.63, 94.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1644 8.00 N 1560 7.00 C 6316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 315.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 74.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 68 through 81 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 92 through 107 removed outlier: 3.664A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 160 through 194 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 265 removed outlier: 3.750A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.889A pdb=" N TYR A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 315 Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 368 through 408 removed outlier: 4.607A pdb=" N THR A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Proline residue: A 393 - end of helix Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 434 through 454 Proline residue: A 443 - end of helix removed outlier: 3.838A pdb=" N MET A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 478 Processing helix chain 'A' and resid 481 through 498 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 536 through 549 Processing helix chain 'A' and resid 569 through 585 Processing helix chain 'A' and resid 590 through 613 removed outlier: 3.681A pdb=" N PHE A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 647 removed outlier: 3.669A pdb=" N GLY A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 677 removed outlier: 3.561A pdb=" N ALA A 661 " --> pdb=" O PRO A 657 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Proline residue: A 663 - end of helix Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 705 through 711 removed outlier: 3.947A pdb=" N ASP A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 92 through 107 removed outlier: 3.664A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 160 through 194 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 242 through 265 removed outlier: 3.750A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.889A pdb=" N TYR B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 315 Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 368 through 408 removed outlier: 4.607A pdb=" N THR B 373 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 423 through 433 Processing helix chain 'B' and resid 434 through 454 Proline residue: B 443 - end of helix removed outlier: 3.838A pdb=" N MET B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 478 Processing helix chain 'B' and resid 481 through 498 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 536 through 549 Processing helix chain 'B' and resid 569 through 585 Processing helix chain 'B' and resid 590 through 613 removed outlier: 3.681A pdb=" N PHE B 594 " --> pdb=" O MET B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 647 removed outlier: 3.669A pdb=" N GLY B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 677 removed outlier: 3.561A pdb=" N ALA B 661 " --> pdb=" O PRO B 657 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 662 " --> pdb=" O PHE B 658 " (cutoff:3.500A) Proline residue: B 663 - end of helix Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 685 through 700 Processing helix chain 'B' and resid 705 through 711 removed outlier: 3.947A pdb=" N ASP B 711 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 207 Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 235 Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 240 removed outlier: 5.096A pdb=" N VAL A 239 " --> pdb=" O MET A 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 204 through 207 Processing sheet with id=AA5, first strand: chain 'B' and resid 233 through 235 Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 240 removed outlier: 5.096A pdb=" N VAL B 239 " --> pdb=" O MET B 321 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1773 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: 1.63 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1480 1.29 - 1.42: 2650 1.42 - 1.55: 5590 1.55 - 1.68: 20 1.68 - 1.81: 88 Bond restraints: 9828 Sorted by residual: bond pdb=" C ILE B 433 " pdb=" O ILE B 433 " ideal model delta sigma weight residual 1.236 1.158 0.078 1.19e-02 7.06e+03 4.27e+01 bond pdb=" C ILE A 433 " pdb=" O ILE A 433 " ideal model delta sigma weight residual 1.236 1.158 0.078 1.19e-02 7.06e+03 4.27e+01 bond pdb=" C MET B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.335 1.386 -0.051 9.40e-03 1.13e+04 2.95e+01 bond pdb=" C MET A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 1.335 1.386 -0.051 9.40e-03 1.13e+04 2.95e+01 bond pdb=" CA PRO B 443 " pdb=" C PRO B 443 " ideal model delta sigma weight residual 1.520 1.455 0.065 1.42e-02 4.96e+03 2.07e+01 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.42: 13220 5.42 - 10.83: 120 10.83 - 16.25: 16 16.25 - 21.66: 2 21.66 - 27.08: 2 Bond angle restraints: 13360 Sorted by residual: angle pdb=" C MET B 76 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " ideal model delta sigma weight residual 120.45 102.99 17.46 1.11e+00 8.12e-01 2.47e+02 angle pdb=" C MET A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta sigma weight residual 120.45 102.99 17.46 1.11e+00 8.12e-01 2.47e+02 angle pdb=" N ILE B 440 " pdb=" CA ILE B 440 " pdb=" C ILE B 440 " ideal model delta sigma weight residual 110.30 98.01 12.29 9.70e-01 1.06e+00 1.61e+02 angle pdb=" N ILE A 440 " pdb=" CA ILE A 440 " pdb=" C ILE A 440 " ideal model delta sigma weight residual 110.30 98.01 12.29 9.70e-01 1.06e+00 1.61e+02 angle pdb=" N ASP A 260 " pdb=" CA ASP A 260 " pdb=" C ASP A 260 " ideal model delta sigma weight residual 112.90 99.48 13.42 1.31e+00 5.83e-01 1.05e+02 ... (remaining 13355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4524 17.71 - 35.41: 562 35.41 - 53.12: 496 53.12 - 70.82: 206 70.82 - 88.53: 26 Dihedral angle restraints: 5814 sinusoidal: 2318 harmonic: 3496 Sorted by residual: dihedral pdb=" N LEU A 549 " pdb=" C LEU A 549 " pdb=" CA LEU A 549 " pdb=" CB LEU A 549 " ideal model delta harmonic sigma weight residual 122.80 137.73 -14.93 0 2.50e+00 1.60e-01 3.57e+01 dihedral pdb=" N LEU B 549 " pdb=" C LEU B 549 " pdb=" CA LEU B 549 " pdb=" CB LEU B 549 " ideal model delta harmonic sigma weight residual 122.80 137.73 -14.93 0 2.50e+00 1.60e-01 3.57e+01 dihedral pdb=" C LEU A 549 " pdb=" N LEU A 549 " pdb=" CA LEU A 549 " pdb=" CB LEU A 549 " ideal model delta harmonic sigma weight residual -122.60 -136.71 14.11 0 2.50e+00 1.60e-01 3.19e+01 ... (remaining 5811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 1374 0.148 - 0.296: 116 0.296 - 0.443: 14 0.443 - 0.591: 4 0.591 - 0.739: 2 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA LEU A 549 " pdb=" N LEU A 549 " pdb=" C LEU A 549 " pdb=" CB LEU A 549 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CA LEU B 549 " pdb=" N LEU B 549 " pdb=" C LEU B 549 " pdb=" CB LEU B 549 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CA MET B 76 " pdb=" N MET B 76 " pdb=" C MET B 76 " pdb=" CB MET B 76 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.29e+00 ... (remaining 1507 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 498 " -0.119 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO A 499 " 0.313 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " -0.103 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " -0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 498 " 0.119 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO B 499 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.103 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 442 " 0.097 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO B 443 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO B 443 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 443 " 0.081 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 184 2.63 - 3.19: 8706 3.19 - 3.76: 16285 3.76 - 4.33: 22808 4.33 - 4.90: 34575 Nonbonded interactions: 82558 Sorted by model distance: nonbonded pdb=" O ARG B 358 " pdb=" CG ARG B 358 " model vdw 2.057 3.440 nonbonded pdb=" O ARG A 358 " pdb=" CG ARG A 358 " model vdw 2.057 3.440 nonbonded pdb=" O ILE A 433 " pdb=" N LYS A 436 " model vdw 2.272 3.120 nonbonded pdb=" O ILE B 433 " pdb=" N LYS B 436 " model vdw 2.272 3.120 nonbonded pdb=" O ILE A 433 " pdb=" N LEU A 435 " model vdw 2.330 3.120 ... (remaining 82553 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 15.460 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4922 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 : 0.008 0.078 9828 Z= 0.595 Angle : 1.418 27.079 13360 Z= 0.925 Chirality : 0.094 0.739 1510 Planarity : 0.011 0.181 1664 Dihedral : 25.414 88.526 3546 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 2.23 % Allowed : 10.62 % Favored : 87.16 % Rotamer: Outliers : 37.57 % Allowed : 13.70 % Favored : 48.73 % Cbeta Deviations : 1.06 % 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: -3.93 (0.19), residues: 1168 helix: -1.78 (0.15), residues: 808 sheet: None (None), residues: 0 loop : -4.38 (0.23), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 697 TYR 0.012 0.001 TYR B 713 PHE 0.026 0.002 PHE B 472 TRP 0.021 0.002 TRP A 75 HIS 0.003 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00794 ( 9828) covalent geometry : angle 1.41755 (13360) hydrogen bonds : bond 0.19109 ( 611) hydrogen bonds : angle 7.12205 ( 1773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 384 poor density : 229 time to evaluate : 0.376 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 231 ASP cc_start: 0.5723 (OUTLIER) cc_final: 0.5266 (p0) REVERT: A 422 ILE cc_start: 0.4704 (OUTLIER) cc_final: 0.4471 (pt) REVERT: A 481 SER cc_start: 0.4253 (OUTLIER) cc_final: 0.3596 (p) REVERT: B 231 ASP cc_start: 0.5730 (OUTLIER) cc_final: 0.5269 (p0) REVERT: B 422 ILE cc_start: 0.4715 (OUTLIER) cc_final: 0.4475 (pt) REVERT: B 481 SER cc_start: 0.4255 (OUTLIER) cc_final: 0.3606 (p) outliers start: 384 outliers final: 54 residues processed: 505 average time/residue: 0.5059 time to fit residues: 275.3284 Evaluate side-chains 217 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 157 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 520 TYR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 703 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 228 ASN A 263 GLN A 269 ASN A 294 HIS A 339 GLN A 398 GLN A 490 GLN A 543 HIS A 561 ASN A 573 GLN A 575 GLN B 208 ASN B 228 ASN B 269 ASN B 294 HIS B 339 GLN B 398 GLN B 490 GLN B 543 HIS B 561 ASN B 573 GLN B 575 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.232706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.191816 restraints weight = 13799.803| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.35 r_work: 0.4125 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9828 Z= 0.198 Angle : 0.814 12.412 13360 Z= 0.410 Chirality : 0.047 0.188 1510 Planarity : 0.007 0.055 1664 Dihedral : 10.121 59.330 1392 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 11.06 % Allowed : 29.35 % Favored : 59.59 % 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: -1.61 (0.24), residues: 1168 helix: 0.06 (0.18), residues: 818 sheet: -4.13 (0.92), residues: 20 loop : -3.73 (0.28), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 331 TYR 0.026 0.002 TYR A 295 PHE 0.024 0.002 PHE B 472 TRP 0.018 0.002 TRP A 75 HIS 0.009 0.002 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9828) covalent geometry : angle 0.81390 (13360) hydrogen bonds : bond 0.05217 ( 611) hydrogen bonds : angle 5.04848 ( 1773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 146 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: A 215 GLU cc_start: 0.5582 (mt-10) cc_final: 0.5316 (mt-10) REVERT: A 231 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8169 (p0) REVERT: A 238 VAL cc_start: 0.5531 (OUTLIER) cc_final: 0.5247 (p) REVERT: A 264 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6511 (pp) REVERT: A 310 ARG cc_start: 0.6008 (ttm170) cc_final: 0.5454 (mtp180) REVERT: A 352 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7336 (pt0) REVERT: A 379 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.3891 (mmp) REVERT: A 550 VAL cc_start: 0.0667 (OUTLIER) cc_final: 0.0258 (p) REVERT: A 658 PHE cc_start: 0.5253 (OUTLIER) cc_final: 0.4862 (t80) REVERT: B 182 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6845 (pp20) REVERT: B 215 GLU cc_start: 0.5577 (mt-10) cc_final: 0.5313 (mt-10) REVERT: B 231 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8158 (p0) REVERT: B 238 VAL cc_start: 0.5527 (OUTLIER) cc_final: 0.5242 (p) REVERT: B 264 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6511 (pp) REVERT: B 310 ARG cc_start: 0.6006 (ttm170) cc_final: 0.5454 (mtp180) REVERT: B 352 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7335 (pt0) REVERT: B 379 MET cc_start: 0.4872 (OUTLIER) cc_final: 0.3895 (mmp) REVERT: B 550 VAL cc_start: 0.0668 (OUTLIER) cc_final: 0.0260 (p) REVERT: B 658 PHE cc_start: 0.5239 (OUTLIER) cc_final: 0.4850 (t80) outliers start: 113 outliers final: 28 residues processed: 232 average time/residue: 0.4623 time to fit residues: 116.6469 Evaluate side-chains 166 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 0.9980 chunk 116 optimal weight: 0.0030 chunk 38 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 111 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 312 ASN A 427 GLN A 546 ASN B 162 HIS B 263 GLN B 312 ASN B 427 GLN B 546 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.228084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.185542 restraints weight = 13570.336| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.32 r_work: 0.4056 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.6905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9828 Z= 0.154 Angle : 0.730 8.794 13360 Z= 0.364 Chirality : 0.043 0.209 1510 Planarity : 0.006 0.056 1664 Dihedral : 8.011 57.779 1334 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 6.65 % Allowed : 33.07 % Favored : 60.27 % 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: -0.39 (0.25), residues: 1168 helix: 0.94 (0.18), residues: 824 sheet: -3.57 (1.04), residues: 20 loop : -3.26 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 468 TYR 0.018 0.001 TYR B 713 PHE 0.017 0.002 PHE A 388 TRP 0.020 0.002 TRP B 75 HIS 0.004 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9828) covalent geometry : angle 0.73048 (13360) hydrogen bonds : bond 0.04753 ( 611) hydrogen bonds : angle 4.61222 ( 1773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 156 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.5771 (mt-10) cc_final: 0.5251 (mp0) REVERT: A 260 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.5504 (m-30) REVERT: A 264 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6592 (pp) REVERT: A 352 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: A 379 MET cc_start: 0.5534 (mmt) cc_final: 0.4846 (mmm) REVERT: A 550 VAL cc_start: 0.0796 (OUTLIER) cc_final: 0.0500 (p) REVERT: A 560 MET cc_start: 0.5774 (pp-130) cc_final: 0.3932 (mpp) REVERT: A 611 ILE cc_start: 0.6769 (pt) cc_final: 0.6440 (pt) REVERT: A 658 PHE cc_start: 0.5263 (OUTLIER) cc_final: 0.4805 (t80) REVERT: A 699 ARG cc_start: 0.7398 (ttp-110) cc_final: 0.7125 (ttp80) REVERT: B 215 GLU cc_start: 0.5764 (mt-10) cc_final: 0.5244 (mp0) REVERT: B 260 ASP cc_start: 0.5828 (OUTLIER) cc_final: 0.5573 (m-30) REVERT: B 264 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6590 (pp) REVERT: B 352 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: B 379 MET cc_start: 0.5529 (mmt) cc_final: 0.4846 (mmm) REVERT: B 550 VAL cc_start: 0.0797 (OUTLIER) cc_final: 0.0501 (p) REVERT: B 560 MET cc_start: 0.5777 (pp-130) cc_final: 0.3937 (mpp) REVERT: B 611 ILE cc_start: 0.6767 (pt) cc_final: 0.6438 (pt) REVERT: B 658 PHE cc_start: 0.5259 (OUTLIER) cc_final: 0.4797 (t80) REVERT: B 699 ARG cc_start: 0.7394 (ttp-110) cc_final: 0.7123 (ttp80) outliers start: 68 outliers final: 14 residues processed: 206 average time/residue: 0.5198 time to fit residues: 115.3476 Evaluate side-chains 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 568 ASN A 616 GLN B 243 ASN B 568 ASN B 616 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.224744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.181322 restraints weight = 13513.633| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.30 r_work: 0.4023 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.7780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9828 Z= 0.159 Angle : 0.723 9.673 13360 Z= 0.356 Chirality : 0.043 0.229 1510 Planarity : 0.005 0.055 1664 Dihedral : 6.433 59.684 1306 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.48 % Allowed : 33.95 % Favored : 60.57 % 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: -0.21 (0.25), residues: 1168 helix: 1.09 (0.18), residues: 828 sheet: -4.09 (0.74), residues: 30 loop : -3.17 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 344 TYR 0.019 0.001 TYR B 713 PHE 0.019 0.002 PHE B 472 TRP 0.017 0.002 TRP B 75 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9828) covalent geometry : angle 0.72314 (13360) hydrogen bonds : bond 0.04603 ( 611) hydrogen bonds : angle 4.57698 ( 1773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7407 (ttm) cc_final: 0.7122 (mtp) REVERT: A 215 GLU cc_start: 0.5823 (mt-10) cc_final: 0.5485 (mt-10) REVERT: A 231 ASP cc_start: 0.8387 (p0) cc_final: 0.8163 (p0) REVERT: A 260 ASP cc_start: 0.5867 (OUTLIER) cc_final: 0.5193 (m-30) REVERT: A 264 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6640 (pp) REVERT: A 352 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: A 389 PHE cc_start: 0.6339 (OUTLIER) cc_final: 0.5736 (t80) REVERT: A 513 LYS cc_start: 0.3750 (OUTLIER) cc_final: 0.3220 (mtmm) REVERT: A 560 MET cc_start: 0.5670 (pp-130) cc_final: 0.3875 (mpp) REVERT: B 82 MET cc_start: 0.7418 (ttm) cc_final: 0.7137 (mtp) REVERT: B 215 GLU cc_start: 0.5818 (mt-10) cc_final: 0.5478 (mt-10) REVERT: B 231 ASP cc_start: 0.8387 (p0) cc_final: 0.8162 (p0) REVERT: B 260 ASP cc_start: 0.5815 (OUTLIER) cc_final: 0.5184 (m-30) REVERT: B 264 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6634 (pp) REVERT: B 352 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: B 389 PHE cc_start: 0.6349 (OUTLIER) cc_final: 0.5728 (t80) REVERT: B 513 LYS cc_start: 0.3745 (OUTLIER) cc_final: 0.3219 (mtmm) REVERT: B 560 MET cc_start: 0.5673 (pp-130) cc_final: 0.3881 (mpp) outliers start: 56 outliers final: 16 residues processed: 194 average time/residue: 0.5073 time to fit residues: 106.5711 Evaluate side-chains 161 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 190 GLN A 243 ASN B 124 ASN B 190 GLN B 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.219648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.175431 restraints weight = 13383.846| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.29 r_work: 0.3961 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.8527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9828 Z= 0.200 Angle : 0.762 10.344 13360 Z= 0.379 Chirality : 0.046 0.332 1510 Planarity : 0.005 0.052 1664 Dihedral : 5.978 59.886 1298 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 6.95 % Allowed : 32.88 % Favored : 60.18 % 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: -0.38 (0.25), residues: 1168 helix: 0.85 (0.18), residues: 838 sheet: -4.32 (0.75), residues: 30 loop : -2.99 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 207 TYR 0.020 0.001 TYR B 713 PHE 0.029 0.002 PHE A 478 TRP 0.018 0.002 TRP A 75 HIS 0.005 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9828) covalent geometry : angle 0.76167 (13360) hydrogen bonds : bond 0.05104 ( 611) hydrogen bonds : angle 4.65472 ( 1773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 136 time to evaluate : 0.405 Fit side-chains REVERT: A 85 ARG cc_start: 0.7084 (mmm160) cc_final: 0.6822 (mmm160) REVERT: A 231 ASP cc_start: 0.8435 (p0) cc_final: 0.8146 (m-30) REVERT: A 264 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6615 (pp) REVERT: A 352 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7447 (pm20) REVERT: A 464 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7205 (tpm170) REVERT: A 565 ILE cc_start: 0.4898 (OUTLIER) cc_final: 0.4661 (pp) REVERT: B 85 ARG cc_start: 0.7097 (mmm160) cc_final: 0.6819 (mmm160) REVERT: B 231 ASP cc_start: 0.8438 (p0) cc_final: 0.8148 (m-30) REVERT: B 260 ASP cc_start: 0.5479 (OUTLIER) cc_final: 0.5205 (m-30) REVERT: B 264 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6606 (pp) REVERT: B 352 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: B 464 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7203 (tpm170) REVERT: B 565 ILE cc_start: 0.4898 (OUTLIER) cc_final: 0.4661 (pp) REVERT: B 611 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6753 (mt) outliers start: 71 outliers final: 20 residues processed: 192 average time/residue: 0.5510 time to fit residues: 113.8482 Evaluate side-chains 151 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 0.4980 chunk 109 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.221680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.177596 restraints weight = 13264.181| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.31 r_work: 0.3989 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.8759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9828 Z= 0.152 Angle : 0.727 12.273 13360 Z= 0.352 Chirality : 0.044 0.315 1510 Planarity : 0.005 0.049 1664 Dihedral : 5.652 56.050 1298 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 6.36 % Allowed : 33.86 % Favored : 59.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.26), residues: 1168 helix: 1.11 (0.18), residues: 840 sheet: -3.90 (0.65), residues: 44 loop : -2.89 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 207 TYR 0.018 0.001 TYR B 713 PHE 0.036 0.002 PHE B 472 TRP 0.015 0.001 TRP B 75 HIS 0.003 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9828) covalent geometry : angle 0.72654 (13360) hydrogen bonds : bond 0.04527 ( 611) hydrogen bonds : angle 4.55693 ( 1773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 140 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.5243 (mtt) cc_final: 0.4939 (ptp) REVERT: A 231 ASP cc_start: 0.8348 (p0) cc_final: 0.8093 (m-30) REVERT: A 264 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6593 (pp) REVERT: A 352 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: A 389 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.6061 (t80) REVERT: A 464 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7687 (ttm-80) REVERT: A 565 ILE cc_start: 0.4814 (OUTLIER) cc_final: 0.4592 (pp) REVERT: B 85 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6758 (mmm160) REVERT: B 114 MET cc_start: 0.5290 (mtt) cc_final: 0.4971 (ptp) REVERT: B 231 ASP cc_start: 0.8346 (p0) cc_final: 0.8094 (m-30) REVERT: B 260 ASP cc_start: 0.5431 (OUTLIER) cc_final: 0.5138 (m-30) REVERT: B 264 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6599 (pp) REVERT: B 352 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: B 389 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.6076 (m-10) REVERT: B 440 ILE cc_start: 0.6291 (OUTLIER) cc_final: 0.6059 (mt) REVERT: B 464 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7677 (ttm-80) REVERT: B 565 ILE cc_start: 0.4814 (OUTLIER) cc_final: 0.4594 (pp) outliers start: 65 outliers final: 20 residues processed: 182 average time/residue: 0.5907 time to fit residues: 115.3265 Evaluate side-chains 161 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 107 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 83 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.222466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.178509 restraints weight = 13432.890| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.31 r_work: 0.4008 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.8964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9828 Z= 0.147 Angle : 0.733 11.042 13360 Z= 0.358 Chirality : 0.044 0.340 1510 Planarity : 0.005 0.047 1664 Dihedral : 5.374 52.142 1298 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.40 % Allowed : 35.62 % Favored : 59.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.26), residues: 1168 helix: 1.14 (0.19), residues: 844 sheet: -3.79 (0.77), residues: 34 loop : -2.74 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 207 TYR 0.016 0.001 TYR B 713 PHE 0.028 0.001 PHE B 472 TRP 0.017 0.001 TRP A 75 HIS 0.003 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9828) covalent geometry : angle 0.73255 (13360) hydrogen bonds : bond 0.04359 ( 611) hydrogen bonds : angle 4.55362 ( 1773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.367 Fit side-chains REVERT: A 114 MET cc_start: 0.5139 (mtt) cc_final: 0.4883 (ptp) REVERT: A 231 ASP cc_start: 0.8252 (p0) cc_final: 0.8052 (m-30) REVERT: A 264 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6568 (pp) REVERT: A 305 GLU cc_start: 0.4787 (pt0) cc_final: 0.4304 (tp30) REVERT: A 310 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5514 (ttm-80) REVERT: A 447 MET cc_start: 0.5301 (mmm) cc_final: 0.5099 (mmm) REVERT: A 449 MET cc_start: 0.5529 (OUTLIER) cc_final: 0.3394 (ttt) REVERT: A 464 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7630 (ttm-80) REVERT: A 565 ILE cc_start: 0.4761 (OUTLIER) cc_final: 0.4518 (pp) REVERT: B 76 MET cc_start: 0.4539 (mtp) cc_final: 0.4276 (tpp) REVERT: B 114 MET cc_start: 0.5239 (mtt) cc_final: 0.4980 (ptp) REVERT: B 231 ASP cc_start: 0.8259 (p0) cc_final: 0.8058 (m-30) REVERT: B 260 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.5153 (m-30) REVERT: B 264 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6595 (pp) REVERT: B 305 GLU cc_start: 0.4784 (pt0) cc_final: 0.4301 (tp30) REVERT: B 310 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5500 (ttm-80) REVERT: B 449 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.3407 (ttt) REVERT: B 464 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7627 (ttm-80) REVERT: B 565 ILE cc_start: 0.4739 (OUTLIER) cc_final: 0.4493 (pp) outliers start: 45 outliers final: 16 residues processed: 169 average time/residue: 0.5660 time to fit residues: 102.9714 Evaluate side-chains 153 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 704 ASN B 315 ASN B 704 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.216020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.171832 restraints weight = 13437.175| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.28 r_work: 0.3930 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.9277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9828 Z= 0.230 Angle : 0.811 11.764 13360 Z= 0.406 Chirality : 0.048 0.410 1510 Planarity : 0.006 0.047 1664 Dihedral : 5.544 51.605 1294 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.99 % Allowed : 35.81 % Favored : 59.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.25), residues: 1168 helix: 0.85 (0.18), residues: 844 sheet: -3.52 (0.87), residues: 34 loop : -2.81 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 85 TYR 0.017 0.002 TYR B 584 PHE 0.028 0.002 PHE B 472 TRP 0.022 0.002 TRP A 75 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 9828) covalent geometry : angle 0.81055 (13360) hydrogen bonds : bond 0.05296 ( 611) hydrogen bonds : angle 4.80349 ( 1773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.416 Fit side-chains REVERT: A 82 MET cc_start: 0.7012 (mtp) cc_final: 0.6440 (ttp) REVERT: A 114 MET cc_start: 0.5182 (mtt) cc_final: 0.4737 (mmm) REVERT: A 240 CYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6815 (p) REVERT: A 264 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6614 (pp) REVERT: A 298 GLU cc_start: 0.3726 (OUTLIER) cc_final: 0.2637 (tm-30) REVERT: A 310 ARG cc_start: 0.5763 (OUTLIER) cc_final: 0.5327 (ttm170) REVERT: A 352 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: A 389 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6155 (m-80) REVERT: A 513 LYS cc_start: 0.4248 (OUTLIER) cc_final: 0.3360 (mtmm) REVERT: B 76 MET cc_start: 0.4722 (mtp) cc_final: 0.4450 (tpp) REVERT: B 114 MET cc_start: 0.5211 (mtt) cc_final: 0.4759 (mmm) REVERT: B 240 CYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6813 (p) REVERT: B 264 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6594 (pp) REVERT: B 298 GLU cc_start: 0.3713 (OUTLIER) cc_final: 0.2630 (tm-30) REVERT: B 310 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.5326 (ttm170) REVERT: B 352 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: B 389 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.6140 (m-10) REVERT: B 464 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7252 (tpm170) outliers start: 51 outliers final: 19 residues processed: 157 average time/residue: 0.5610 time to fit residues: 94.9000 Evaluate side-chains 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 513 LYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 160 TRP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.220117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.176766 restraints weight = 13394.888| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.26 r_work: 0.3997 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.9440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9828 Z= 0.154 Angle : 0.755 11.879 13360 Z= 0.372 Chirality : 0.044 0.328 1510 Planarity : 0.005 0.045 1664 Dihedral : 5.230 48.650 1294 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.84 % Allowed : 37.67 % Favored : 59.49 % 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: -0.01 (0.25), residues: 1168 helix: 1.03 (0.18), residues: 844 sheet: -3.13 (0.88), residues: 34 loop : -2.70 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 85 TYR 0.015 0.001 TYR A 713 PHE 0.026 0.002 PHE A 472 TRP 0.017 0.001 TRP A 75 HIS 0.003 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9828) covalent geometry : angle 0.75539 (13360) hydrogen bonds : bond 0.04494 ( 611) hydrogen bonds : angle 4.68443 ( 1773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.394 Fit side-chains REVERT: A 85 ARG cc_start: 0.7135 (mmm160) cc_final: 0.6407 (mmm160) REVERT: A 305 GLU cc_start: 0.4802 (pt0) cc_final: 0.4399 (tp30) REVERT: A 389 PHE cc_start: 0.6409 (OUTLIER) cc_final: 0.6097 (m-80) REVERT: A 660 ILE cc_start: 0.8142 (tt) cc_final: 0.7708 (pp) REVERT: B 85 ARG cc_start: 0.7103 (mmm160) cc_final: 0.6372 (mmm160) REVERT: B 305 GLU cc_start: 0.4793 (pt0) cc_final: 0.4392 (tp30) REVERT: B 389 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.6085 (m-80) REVERT: B 449 MET cc_start: 0.6451 (mtt) cc_final: 0.6153 (ptp) REVERT: B 464 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7606 (ttm-80) REVERT: B 660 ILE cc_start: 0.8150 (tt) cc_final: 0.7724 (pp) outliers start: 29 outliers final: 15 residues processed: 149 average time/residue: 0.5885 time to fit residues: 94.2795 Evaluate side-chains 140 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 116 optimal weight: 0.0770 chunk 53 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.222511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.179659 restraints weight = 13350.725| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.25 r_work: 0.4030 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.9580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9828 Z= 0.140 Angle : 0.741 11.708 13360 Z= 0.363 Chirality : 0.043 0.304 1510 Planarity : 0.005 0.045 1664 Dihedral : 5.019 46.957 1294 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.25 % Allowed : 38.94 % Favored : 58.81 % 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: 0.24 (0.26), residues: 1168 helix: 1.19 (0.19), residues: 844 sheet: -2.61 (0.88), residues: 34 loop : -2.61 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 85 TYR 0.014 0.001 TYR B 713 PHE 0.022 0.001 PHE B 472 TRP 0.018 0.001 TRP A 625 HIS 0.003 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9828) covalent geometry : angle 0.74085 (13360) hydrogen bonds : bond 0.04211 ( 611) hydrogen bonds : angle 4.60208 ( 1773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.389 Fit side-chains REVERT: A 114 MET cc_start: 0.5417 (ptp) cc_final: 0.4654 (tpt) REVERT: A 305 GLU cc_start: 0.4931 (pt0) cc_final: 0.4574 (tp30) REVERT: A 447 MET cc_start: 0.5348 (mmm) cc_final: 0.4996 (mmm) REVERT: A 449 MET cc_start: 0.6974 (mtt) cc_final: 0.6664 (ptp) REVERT: A 464 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7440 (ttm170) REVERT: A 660 ILE cc_start: 0.8181 (tt) cc_final: 0.7754 (pp) REVERT: A 676 ARG cc_start: 0.7896 (tpp80) cc_final: 0.7262 (tpt90) REVERT: B 85 ARG cc_start: 0.7229 (mmm160) cc_final: 0.6485 (mmm160) REVERT: B 114 MET cc_start: 0.5352 (ptp) cc_final: 0.4583 (mmm) REVERT: B 305 GLU cc_start: 0.4928 (pt0) cc_final: 0.4570 (tp30) REVERT: B 449 MET cc_start: 0.6697 (mtt) cc_final: 0.6493 (ptp) REVERT: B 464 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7593 (ttm170) REVERT: B 660 ILE cc_start: 0.8178 (tt) cc_final: 0.7749 (pp) outliers start: 23 outliers final: 9 residues processed: 152 average time/residue: 0.5154 time to fit residues: 84.7435 Evaluate side-chains 130 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 68 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.221401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.178169 restraints weight = 13318.108| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.26 r_work: 0.4014 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.9685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9828 Z= 0.147 Angle : 0.749 11.628 13360 Z= 0.365 Chirality : 0.044 0.328 1510 Planarity : 0.005 0.044 1664 Dihedral : 4.797 47.025 1292 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.57 % Allowed : 40.12 % Favored : 58.32 % 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: 0.20 (0.25), residues: 1168 helix: 1.25 (0.19), residues: 832 sheet: -2.60 (0.86), residues: 36 loop : -2.77 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 85 TYR 0.016 0.001 TYR B 713 PHE 0.018 0.001 PHE B 472 TRP 0.016 0.001 TRP A 75 HIS 0.003 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9828) covalent geometry : angle 0.74887 (13360) hydrogen bonds : bond 0.04290 ( 611) hydrogen bonds : angle 4.55087 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4702.94 seconds wall clock time: 80 minutes 51.40 seconds (4851.40 seconds total)