Starting phenix.real_space_refine on Wed Apr 30 08:43:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qpc_4613/04_2025/6qpc_4613.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qpc_4613/04_2025/6qpc_4613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qpc_4613/04_2025/6qpc_4613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qpc_4613/04_2025/6qpc_4613.map" model { file = "/net/cci-nas-00/data/ceres_data/6qpc_4613/04_2025/6qpc_4613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qpc_4613/04_2025/6qpc_4613.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 62 5.16 5 C 6040 2.51 5 N 1454 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9140 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4530 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 28, 'TRANS': 548} Chain breaks: 10 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 126 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'P1O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 8.53, per 1000 atoms: 0.93 Number of scatterers: 9140 At special positions: 0 Unit cell: (94.116, 110.308, 109.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 62 16.00 P 2 15.00 O 1578 8.00 N 1454 7.00 C 6040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.02 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.02 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.02 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.6 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 2 sheets defined 70.3% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.556A pdb=" N ARG A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.533A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.914A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 375 removed outlier: 4.376A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 404 removed outlier: 3.620A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 487 removed outlier: 3.667A pdb=" N ILE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 Processing helix chain 'A' and resid 543 through 573 removed outlier: 4.855A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 637 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.656A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 687 through 710 removed outlier: 3.854A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.750A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.516A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.600A pdb=" N ASN A 779 " --> pdb=" O GLY A 775 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 265 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.533A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.914A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 375 removed outlier: 4.375A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 404 removed outlier: 3.620A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 487 removed outlier: 3.666A pdb=" N ILE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 Processing helix chain 'B' and resid 543 through 573 removed outlier: 4.854A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 637 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.657A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 687 through 710 removed outlier: 3.855A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.751A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 removed outlier: 3.516A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.601A pdb=" N ASN B 779 " --> pdb=" O GLY B 775 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing sheet with id=AA1, first strand: chain 'A' and resid 782 through 783 Processing sheet with id=AA2, first strand: chain 'B' and resid 782 through 783 592 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1464 1.32 - 1.45: 2722 1.45 - 1.58: 5080 1.58 - 1.71: 6 1.71 - 1.83: 100 Bond restraints: 9372 Sorted by residual: bond pdb=" O3 P1O A1003 " pdb=" P1 P1O A1003 " ideal model delta sigma weight residual 1.648 1.770 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" O3 P1O B1003 " pdb=" P1 P1O B1003 " ideal model delta sigma weight residual 1.648 1.770 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C19 P1O A1003 " pdb=" C20 P1O A1003 " ideal model delta sigma weight residual 1.502 1.584 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C19 P1O B1003 " pdb=" C20 P1O B1003 " ideal model delta sigma weight residual 1.502 1.583 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 P1O B1003 " pdb=" C2 P1O B1003 " ideal model delta sigma weight residual 1.513 1.589 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 9367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 12234 2.26 - 4.52: 418 4.52 - 6.78: 50 6.78 - 9.04: 26 9.04 - 11.30: 6 Bond angle restraints: 12734 Sorted by residual: angle pdb=" CA TYR A 477 " pdb=" CB TYR A 477 " pdb=" CG TYR A 477 " ideal model delta sigma weight residual 113.90 122.44 -8.54 1.80e+00 3.09e-01 2.25e+01 angle pdb=" CA TYR B 477 " pdb=" CB TYR B 477 " pdb=" CG TYR B 477 " ideal model delta sigma weight residual 113.90 122.42 -8.52 1.80e+00 3.09e-01 2.24e+01 angle pdb=" C LEU B 503 " pdb=" N THR B 504 " pdb=" CA THR B 504 " ideal model delta sigma weight residual 121.62 128.96 -7.34 1.57e+00 4.06e-01 2.18e+01 angle pdb=" C LEU A 503 " pdb=" N THR A 504 " pdb=" CA THR A 504 " ideal model delta sigma weight residual 121.62 128.94 -7.32 1.57e+00 4.06e-01 2.17e+01 angle pdb=" C VAL A 484 " pdb=" N PHE A 485 " pdb=" CA PHE A 485 " ideal model delta sigma weight residual 120.29 113.76 6.53 1.42e+00 4.96e-01 2.11e+01 ... (remaining 12729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.87: 5251 27.87 - 55.73: 227 55.73 - 83.60: 18 83.60 - 111.47: 2 111.47 - 139.34: 2 Dihedral angle restraints: 5500 sinusoidal: 2100 harmonic: 3400 Sorted by residual: dihedral pdb=" CA ARG A 354 " pdb=" C ARG A 354 " pdb=" N LEU A 355 " pdb=" CA LEU A 355 " ideal model delta harmonic sigma weight residual -180.00 -131.65 -48.35 0 5.00e+00 4.00e-02 9.35e+01 dihedral pdb=" CA ARG B 354 " pdb=" C ARG B 354 " pdb=" N LEU B 355 " pdb=" CA LEU B 355 " ideal model delta harmonic sigma weight residual 180.00 -131.70 -48.30 0 5.00e+00 4.00e-02 9.33e+01 dihedral pdb=" CA CYS A 356 " pdb=" C CYS A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual -180.00 -142.63 -37.37 0 5.00e+00 4.00e-02 5.59e+01 ... (remaining 5497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.016: 1424 1.016 - 2.032: 0 2.032 - 3.048: 0 3.048 - 4.064: 0 4.064 - 5.080: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C7 P1O B1003 " pdb=" C6 P1O B1003 " pdb=" C8 P1O B1003 " pdb=" O7 P1O B1003 " both_signs ideal model delta sigma weight residual False -2.35 2.73 -5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C7 P1O A1003 " pdb=" C6 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " both_signs ideal model delta sigma weight residual False -2.35 2.73 -5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" CB VAL A 531 " pdb=" CA VAL A 531 " pdb=" CG1 VAL A 531 " pdb=" CG2 VAL A 531 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1423 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 670 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C GLU A 670 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU A 670 " -0.019 2.00e-02 2.50e+03 pdb=" N MET A 671 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 670 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C GLU B 670 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU B 670 " 0.019 2.00e-02 2.50e+03 pdb=" N MET B 671 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 668 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C TYR A 668 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR A 668 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 669 " 0.017 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 516 2.72 - 3.27: 9447 3.27 - 3.81: 15769 3.81 - 4.36: 18137 4.36 - 4.90: 31147 Nonbonded interactions: 75016 Sorted by model distance: nonbonded pdb=" O VAL A 561 " pdb=" OG SER A 565 " model vdw 2.176 3.040 nonbonded pdb=" O VAL B 561 " pdb=" OG SER B 565 " model vdw 2.178 3.040 nonbonded pdb=" O ALA B 508 " pdb=" OG1 THR B 512 " model vdw 2.290 3.040 nonbonded pdb=" O ALA A 508 " pdb=" OG1 THR A 512 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR A 364 " pdb=" OG SER A 367 " model vdw 2.304 3.040 ... (remaining 75011 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: 0.05 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.200 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.009 0.122 9384 Z= 0.393 Angle : 1.016 11.295 12754 Z= 0.551 Chirality : 0.198 5.080 1426 Planarity : 0.009 0.069 1564 Dihedral : 15.204 139.337 3270 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.22 % Allowed : 6.06 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.19), residues: 1110 helix: -2.06 (0.14), residues: 760 sheet: None (None), residues: 0 loop : -2.19 (0.26), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 397 HIS 0.004 0.001 HIS A 830 PHE 0.032 0.003 PHE B 685 TYR 0.042 0.003 TYR B 580 ARG 0.004 0.001 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.12833 ( 592) hydrogen bonds : angle 7.51760 ( 1758) SS BOND : bond 0.00618 ( 10) SS BOND : angle 2.70478 ( 20) covalent geometry : bond 0.00867 ( 9372) covalent geometry : angle 1.01130 (12734) Misc. bond : bond 0.00175 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.8079 (tt0) cc_final: 0.7755 (tt0) REVERT: A 355 LEU cc_start: 0.5820 (tp) cc_final: 0.5102 (pt) REVERT: A 524 LEU cc_start: 0.8983 (tp) cc_final: 0.8671 (mt) REVERT: A 534 MET cc_start: 0.7100 (mtm) cc_final: 0.6763 (mtt) REVERT: A 650 TRP cc_start: 0.7373 (p90) cc_final: 0.6969 (p90) REVERT: A 695 ASN cc_start: 0.8817 (t0) cc_final: 0.8504 (t0) REVERT: A 730 GLN cc_start: 0.8584 (mt0) cc_final: 0.8269 (mm-40) REVERT: A 818 HIS cc_start: 0.6650 (t-90) cc_final: 0.6259 (t70) REVERT: B 294 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6223 (mm-30) REVERT: B 355 LEU cc_start: 0.5826 (tp) cc_final: 0.5268 (pt) REVERT: B 534 MET cc_start: 0.6973 (mtm) cc_final: 0.6652 (ptt) REVERT: B 650 TRP cc_start: 0.7392 (p90) cc_final: 0.6960 (p90) REVERT: B 661 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8274 (mmmm) REVERT: B 730 GLN cc_start: 0.8561 (mt0) cc_final: 0.8262 (mm-40) outliers start: 2 outliers final: 2 residues processed: 216 average time/residue: 0.2027 time to fit residues: 61.0770 Evaluate side-chains 151 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN A 608 GLN A 695 ASN A 730 GLN B 544 GLN B 608 GLN B 695 ASN B 730 GLN B 818 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.140590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.119511 restraints weight = 18521.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121695 restraints weight = 11827.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.122947 restraints weight = 8911.243| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9384 Z= 0.152 Angle : 0.631 8.747 12754 Z= 0.338 Chirality : 0.041 0.158 1426 Planarity : 0.006 0.059 1564 Dihedral : 10.136 150.230 1308 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.87 % Allowed : 11.12 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1110 helix: -0.18 (0.16), residues: 750 sheet: None (None), residues: 0 loop : -1.67 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.008 0.001 HIS B 818 PHE 0.027 0.002 PHE A 485 TYR 0.030 0.002 TYR B 477 ARG 0.005 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.05188 ( 592) hydrogen bonds : angle 5.29236 ( 1758) SS BOND : bond 0.00213 ( 10) SS BOND : angle 1.34435 ( 20) covalent geometry : bond 0.00321 ( 9372) covalent geometry : angle 0.62943 (12734) Misc. bond : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.920 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 517 SER cc_start: 0.9006 (p) cc_final: 0.8780 (t) REVERT: B 265 GLU cc_start: 0.7372 (tt0) cc_final: 0.7167 (tt0) REVERT: B 524 LEU cc_start: 0.8798 (tp) cc_final: 0.8523 (mt) outliers start: 17 outliers final: 12 residues processed: 185 average time/residue: 0.1818 time to fit residues: 48.6031 Evaluate side-chains 160 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 694 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS B 695 ASN B 818 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.139027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117972 restraints weight = 18848.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.120182 restraints weight = 11991.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121130 restraints weight = 9014.614| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9384 Z= 0.177 Angle : 0.614 8.705 12754 Z= 0.328 Chirality : 0.041 0.146 1426 Planarity : 0.005 0.055 1564 Dihedral : 9.674 150.484 1306 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.87 % Allowed : 14.98 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1110 helix: 0.49 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 650 HIS 0.005 0.001 HIS B 844 PHE 0.024 0.002 PHE B 485 TYR 0.027 0.002 TYR B 477 ARG 0.004 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.05042 ( 592) hydrogen bonds : angle 4.98188 ( 1758) SS BOND : bond 0.00280 ( 10) SS BOND : angle 1.03994 ( 20) covalent geometry : bond 0.00387 ( 9372) covalent geometry : angle 0.61281 (12734) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7406 (tt0) cc_final: 0.7199 (tt0) REVERT: A 305 TYR cc_start: 0.8291 (t80) cc_final: 0.7621 (t80) REVERT: A 322 LEU cc_start: 0.8459 (mm) cc_final: 0.8001 (tt) REVERT: B 305 TYR cc_start: 0.8283 (t80) cc_final: 0.7623 (t80) REVERT: B 474 ILE cc_start: 0.8296 (mm) cc_final: 0.7817 (mm) outliers start: 17 outliers final: 13 residues processed: 170 average time/residue: 0.1967 time to fit residues: 49.9879 Evaluate side-chains 158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 694 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 10.0000 chunk 110 optimal weight: 0.0270 chunk 59 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN B 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.140980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120194 restraints weight = 18522.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.122194 restraints weight = 11773.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.123738 restraints weight = 8928.689| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9384 Z= 0.141 Angle : 0.574 8.656 12754 Z= 0.307 Chirality : 0.040 0.145 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.522 151.463 1306 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.53 % Allowed : 15.42 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1110 helix: 0.84 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.14 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 650 HIS 0.009 0.001 HIS B 818 PHE 0.021 0.002 PHE B 485 TYR 0.030 0.001 TYR B 477 ARG 0.003 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 592) hydrogen bonds : angle 4.77836 ( 1758) SS BOND : bond 0.00189 ( 10) SS BOND : angle 0.90278 ( 20) covalent geometry : bond 0.00301 ( 9372) covalent geometry : angle 0.57325 (12734) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 821 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6512 (pp20) REVERT: B 305 TYR cc_start: 0.8279 (t80) cc_final: 0.7551 (t80) REVERT: B 322 LEU cc_start: 0.8377 (mm) cc_final: 0.7903 (tt) REVERT: B 821 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6574 (pm20) outliers start: 23 outliers final: 18 residues processed: 188 average time/residue: 0.1808 time to fit residues: 49.5880 Evaluate side-chains 166 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 30.0000 chunk 70 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.140238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.118591 restraints weight = 18751.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120831 restraints weight = 11880.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.122221 restraints weight = 8918.042| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9384 Z= 0.161 Angle : 0.587 8.739 12754 Z= 0.313 Chirality : 0.040 0.162 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.397 151.275 1306 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.19 % Allowed : 16.30 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1110 helix: 1.01 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.08 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 829 HIS 0.003 0.001 HIS A 818 PHE 0.020 0.002 PHE B 485 TYR 0.026 0.001 TYR B 477 ARG 0.006 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 592) hydrogen bonds : angle 4.70097 ( 1758) SS BOND : bond 0.00266 ( 10) SS BOND : angle 0.99881 ( 20) covalent geometry : bond 0.00354 ( 9372) covalent geometry : angle 0.58657 (12734) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.8338 (t80) cc_final: 0.7780 (t80) REVERT: A 322 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8029 (tt) REVERT: A 373 ILE cc_start: 0.8362 (mt) cc_final: 0.8144 (mt) REVERT: B 524 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8574 (mt) REVERT: B 821 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6431 (pm20) outliers start: 29 outliers final: 18 residues processed: 175 average time/residue: 0.1781 time to fit residues: 45.5773 Evaluate side-chains 167 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 57 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.140690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.119410 restraints weight = 18652.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121430 restraints weight = 12000.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.122937 restraints weight = 9194.741| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9384 Z= 0.148 Angle : 0.593 11.274 12754 Z= 0.308 Chirality : 0.040 0.154 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.331 151.753 1306 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.41 % Allowed : 17.18 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.24), residues: 1110 helix: 1.12 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.91 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 397 HIS 0.004 0.001 HIS B 818 PHE 0.018 0.002 PHE B 485 TYR 0.029 0.001 TYR B 477 ARG 0.003 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 592) hydrogen bonds : angle 4.67119 ( 1758) SS BOND : bond 0.00228 ( 10) SS BOND : angle 0.91269 ( 20) covalent geometry : bond 0.00321 ( 9372) covalent geometry : angle 0.59209 (12734) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8027 (tt) REVERT: A 373 ILE cc_start: 0.8381 (mt) cc_final: 0.8104 (mt) REVERT: A 821 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6444 (pp20) REVERT: A 842 MET cc_start: 0.8469 (ttt) cc_final: 0.8235 (ttt) REVERT: B 305 TYR cc_start: 0.8306 (t80) cc_final: 0.7733 (t80) REVERT: B 322 LEU cc_start: 0.8431 (mm) cc_final: 0.7976 (tt) REVERT: B 373 ILE cc_start: 0.8423 (mt) cc_final: 0.8134 (mt) REVERT: B 524 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8556 (mt) REVERT: B 821 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6390 (pm20) outliers start: 31 outliers final: 18 residues processed: 186 average time/residue: 0.1685 time to fit residues: 46.4636 Evaluate side-chains 174 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.142313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.120994 restraints weight = 18833.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123248 restraints weight = 11930.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124791 restraints weight = 8918.930| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9384 Z= 0.132 Angle : 0.593 11.523 12754 Z= 0.311 Chirality : 0.041 0.176 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.251 152.440 1306 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.08 % Allowed : 18.39 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1110 helix: 1.20 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.82 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.006 0.001 HIS A 818 PHE 0.017 0.001 PHE B 485 TYR 0.028 0.001 TYR B 477 ARG 0.002 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 592) hydrogen bonds : angle 4.63955 ( 1758) SS BOND : bond 0.00168 ( 10) SS BOND : angle 0.95112 ( 20) covalent geometry : bond 0.00281 ( 9372) covalent geometry : angle 0.59266 (12734) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.8302 (t80) cc_final: 0.7931 (t80) REVERT: A 322 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8002 (tt) REVERT: A 373 ILE cc_start: 0.8306 (mt) cc_final: 0.8014 (mt) REVERT: A 477 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6324 (p90) REVERT: A 821 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6431 (pp20) REVERT: B 305 TYR cc_start: 0.8280 (t80) cc_final: 0.7554 (t80) REVERT: B 322 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7957 (tt) REVERT: B 373 ILE cc_start: 0.8349 (mt) cc_final: 0.8018 (mt) REVERT: B 524 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8572 (mt) REVERT: B 812 PHE cc_start: 0.8131 (m-80) cc_final: 0.7880 (m-80) REVERT: B 821 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6380 (pm20) outliers start: 28 outliers final: 14 residues processed: 188 average time/residue: 0.1709 time to fit residues: 47.1345 Evaluate side-chains 170 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120756 restraints weight = 19006.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122767 restraints weight = 12140.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124351 restraints weight = 9244.304| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9384 Z= 0.161 Angle : 0.616 11.865 12754 Z= 0.321 Chirality : 0.041 0.188 1426 Planarity : 0.005 0.054 1564 Dihedral : 9.205 151.417 1306 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.41 % Allowed : 18.94 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1110 helix: 1.20 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.82 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 650 HIS 0.007 0.001 HIS B 818 PHE 0.017 0.002 PHE B 485 TYR 0.027 0.001 TYR B 477 ARG 0.002 0.000 ARG B 753 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 592) hydrogen bonds : angle 4.67547 ( 1758) SS BOND : bond 0.00214 ( 10) SS BOND : angle 0.97967 ( 20) covalent geometry : bond 0.00357 ( 9372) covalent geometry : angle 0.61555 (12734) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7962 (tt) REVERT: A 373 ILE cc_start: 0.8378 (mt) cc_final: 0.8072 (mt) REVERT: A 477 TYR cc_start: 0.6721 (OUTLIER) cc_final: 0.6247 (p90) REVERT: A 553 MET cc_start: 0.8180 (tpp) cc_final: 0.7918 (tpp) REVERT: A 821 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6440 (pm20) REVERT: B 322 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8012 (tt) REVERT: B 373 ILE cc_start: 0.8348 (mt) cc_final: 0.8012 (mt) REVERT: B 821 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6463 (pm20) outliers start: 31 outliers final: 20 residues processed: 175 average time/residue: 0.1822 time to fit residues: 46.7315 Evaluate side-chains 174 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 57 optimal weight: 30.0000 chunk 96 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.141696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120586 restraints weight = 18623.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.122778 restraints weight = 12005.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124045 restraints weight = 9052.141| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9384 Z= 0.162 Angle : 0.619 12.097 12754 Z= 0.322 Chirality : 0.041 0.148 1426 Planarity : 0.005 0.055 1564 Dihedral : 9.226 151.599 1306 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.97 % Allowed : 19.71 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1110 helix: 1.26 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.84 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 650 HIS 0.009 0.001 HIS B 818 PHE 0.017 0.001 PHE B 485 TYR 0.027 0.001 TYR B 477 ARG 0.002 0.000 ARG B 289 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 592) hydrogen bonds : angle 4.67652 ( 1758) SS BOND : bond 0.00217 ( 10) SS BOND : angle 0.98768 ( 20) covalent geometry : bond 0.00362 ( 9372) covalent geometry : angle 0.61868 (12734) Misc. bond : bond 0.00020 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 373 ILE cc_start: 0.8357 (mt) cc_final: 0.8021 (mt) REVERT: A 477 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.6262 (p90) REVERT: A 553 MET cc_start: 0.8229 (tpp) cc_final: 0.7919 (tpp) REVERT: A 821 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6432 (pm20) REVERT: B 322 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7963 (tt) REVERT: B 373 ILE cc_start: 0.8331 (mt) cc_final: 0.8003 (mt) REVERT: B 821 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6429 (pm20) outliers start: 27 outliers final: 18 residues processed: 172 average time/residue: 0.1762 time to fit residues: 45.6036 Evaluate side-chains 167 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 0.0170 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.144469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.123492 restraints weight = 18708.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.125467 restraints weight = 12111.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127161 restraints weight = 9295.076| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9384 Z= 0.131 Angle : 0.609 12.722 12754 Z= 0.312 Chirality : 0.041 0.160 1426 Planarity : 0.005 0.055 1564 Dihedral : 9.154 152.983 1306 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.98 % Allowed : 21.26 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1110 helix: 1.32 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 650 HIS 0.004 0.001 HIS B 818 PHE 0.016 0.001 PHE B 485 TYR 0.025 0.001 TYR B 477 ARG 0.003 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 592) hydrogen bonds : angle 4.58523 ( 1758) SS BOND : bond 0.00137 ( 10) SS BOND : angle 0.90365 ( 20) covalent geometry : bond 0.00281 ( 9372) covalent geometry : angle 0.60890 (12734) Misc. bond : bond 0.00016 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.974 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 322 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7988 (tt) REVERT: A 373 ILE cc_start: 0.8334 (mt) cc_final: 0.7994 (mt) REVERT: A 477 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.6364 (p90) REVERT: A 553 MET cc_start: 0.8129 (tpp) cc_final: 0.7794 (tpp) REVERT: A 821 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6360 (pm20) REVERT: B 322 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7900 (tt) REVERT: B 373 ILE cc_start: 0.8269 (mt) cc_final: 0.7900 (mt) REVERT: B 821 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6415 (pm20) outliers start: 18 outliers final: 10 residues processed: 175 average time/residue: 0.1723 time to fit residues: 44.8567 Evaluate side-chains 165 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123162 restraints weight = 18584.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125425 restraints weight = 12078.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126724 restraints weight = 9047.103| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9384 Z= 0.141 Angle : 0.646 12.000 12754 Z= 0.330 Chirality : 0.041 0.195 1426 Planarity : 0.005 0.056 1564 Dihedral : 9.092 152.373 1306 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.87 % Allowed : 22.03 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1110 helix: 1.33 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.63 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 650 HIS 0.004 0.001 HIS B 818 PHE 0.035 0.001 PHE B 556 TYR 0.023 0.001 TYR B 477 ARG 0.002 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 592) hydrogen bonds : angle 4.57353 ( 1758) SS BOND : bond 0.00174 ( 10) SS BOND : angle 0.92491 ( 20) covalent geometry : bond 0.00314 ( 9372) covalent geometry : angle 0.64575 (12734) Misc. bond : bond 0.00013 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2925.94 seconds wall clock time: 51 minutes 53.46 seconds (3113.46 seconds total)