Starting phenix.real_space_refine on Tue Feb 11 18:30:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s1z_24813/02_2025/7s1z_24813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s1z_24813/02_2025/7s1z_24813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s1z_24813/02_2025/7s1z_24813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s1z_24813/02_2025/7s1z_24813.map" model { file = "/net/cci-nas-00/data/ceres_data/7s1z_24813/02_2025/7s1z_24813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s1z_24813/02_2025/7s1z_24813.cif" } resolution = 3.3 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= 0.010 sd= 0.150 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 34 5.16 5 C 4224 2.51 5 N 1034 2.21 5 O 1124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6416 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3208 Classifications: {'peptide': 472} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 83} Link IDs: {'PTRANS': 15, 'TRANS': 456} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 208 Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3208 Classifications: {'peptide': 472} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 83} Link IDs: {'PTRANS': 15, 'TRANS': 456} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 208 Time building chain proxies: 4.51, per 1000 atoms: 0.70 Number of scatterers: 6416 At special positions: 0 Unit cell: (104.94, 83.74, 87.98, 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 34 16.00 O 1124 8.00 N 1034 7.00 C 4224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 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: 1.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 71.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 288 through 300 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.532A pdb=" N PHE A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.532A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 344 removed outlier: 4.115A pdb=" N LEU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 398 removed outlier: 4.508A pdb=" N GLY A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.502A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 454 removed outlier: 3.650A pdb=" N ALA A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.651A pdb=" N LYS A 460 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 461 " --> pdb=" O GLU A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 461' Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 500 through 506 removed outlier: 4.358A pdb=" N GLY A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 516 through 542 Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.599A pdb=" N CYS A 568 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 570 " --> pdb=" O ALA A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.562A pdb=" N SER A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 630 removed outlier: 3.647A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 654 through 667 removed outlier: 4.131A pdb=" N THR A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 699 removed outlier: 4.242A pdb=" N ILE A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 730 Processing helix chain 'A' and resid 731 through 753 Processing helix chain 'B' and resid 288 through 300 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.441A pdb=" N PHE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.511A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 344 removed outlier: 4.170A pdb=" N LEU B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 398 removed outlier: 4.482A pdb=" N GLY B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.654A pdb=" N ILE B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 454 removed outlier: 3.639A pdb=" N ALA B 432 " --> pdb=" O MET B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.646A pdb=" N LYS B 460 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B 461 " --> pdb=" O GLU B 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 461' Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 500 removed outlier: 5.936A pdb=" N GLY B 500 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.585A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 516 through 542 Processing helix chain 'B' and resid 565 through 570 removed outlier: 3.598A pdb=" N CYS B 568 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 570 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.529A pdb=" N SER B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 630 removed outlier: 3.526A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.964A pdb=" N THR B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 699 removed outlier: 3.924A pdb=" N ILE B 677 " --> pdb=" O VAL B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 730 removed outlier: 3.505A pdb=" N SER B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 753 473 hydrogen bonds defined for protein. 1395 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: 1.72 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2004 1.34 - 1.46: 1560 1.46 - 1.58: 2948 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 6560 Sorted by residual: bond pdb=" CG1 ILE B 747 " pdb=" CD1 ILE B 747 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.44e+00 bond pdb=" CG1 ILE A 747 " pdb=" CD1 ILE A 747 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.22e+00 bond pdb=" C ALA B 675 " pdb=" N PRO B 676 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.51e-02 4.39e+03 1.91e+00 bond pdb=" C ALA A 675 " pdb=" N PRO A 676 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.51e-02 4.39e+03 1.76e+00 bond pdb=" C PHE A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.333 1.351 -0.018 1.44e-02 4.82e+03 1.59e+00 ... (remaining 6555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 8568 1.45 - 2.91: 318 2.91 - 4.36: 68 4.36 - 5.81: 16 5.81 - 7.27: 10 Bond angle restraints: 8980 Sorted by residual: angle pdb=" N ILE A 507 " pdb=" CA ILE A 507 " pdb=" C ILE A 507 " ideal model delta sigma weight residual 112.80 106.16 6.64 1.15e+00 7.56e-01 3.33e+01 angle pdb=" N ILE B 507 " pdb=" CA ILE B 507 " pdb=" C ILE B 507 " ideal model delta sigma weight residual 113.07 107.03 6.04 1.36e+00 5.41e-01 1.97e+01 angle pdb=" N ILE B 556 " pdb=" CA ILE B 556 " pdb=" C ILE B 556 " ideal model delta sigma weight residual 111.91 108.72 3.19 8.90e-01 1.26e+00 1.28e+01 angle pdb=" N ILE A 556 " pdb=" CA ILE A 556 " pdb=" C ILE A 556 " ideal model delta sigma weight residual 111.91 108.85 3.06 8.90e-01 1.26e+00 1.18e+01 angle pdb=" N SER A 516 " pdb=" CA SER A 516 " pdb=" C SER A 516 " ideal model delta sigma weight residual 112.72 109.19 3.53 1.28e+00 6.10e-01 7.60e+00 ... (remaining 8975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 3350 16.22 - 32.45: 255 32.45 - 48.67: 50 48.67 - 64.89: 3 64.89 - 81.12: 4 Dihedral angle restraints: 3662 sinusoidal: 1056 harmonic: 2606 Sorted by residual: dihedral pdb=" CB CYS B 577 " pdb=" SG CYS B 577 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual 93.00 21.59 71.41 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 21.64 71.36 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA GLY A 286 " pdb=" C GLY A 286 " pdb=" N TRP A 287 " pdb=" CA TRP A 287 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 3659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 555 0.026 - 0.052: 309 0.052 - 0.079: 162 0.079 - 0.105: 58 0.105 - 0.131: 10 Chirality restraints: 1094 Sorted by residual: chirality pdb=" CG LEU B 743 " pdb=" CB LEU B 743 " pdb=" CD1 LEU B 743 " pdb=" CD2 LEU B 743 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CG LEU A 743 " pdb=" CB LEU A 743 " pdb=" CD1 LEU A 743 " pdb=" CD2 LEU A 743 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE B 507 " pdb=" N ILE B 507 " pdb=" C ILE B 507 " pdb=" CB ILE B 507 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1091 not shown) Planarity restraints: 1126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 705 " -0.065 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO B 706 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 706 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 706 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 675 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO B 676 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 676 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 676 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 675 " -0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 676 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.046 5.00e-02 4.00e+02 ... (remaining 1123 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1424 2.78 - 3.31: 6932 3.31 - 3.84: 10887 3.84 - 4.37: 11091 4.37 - 4.90: 19946 Nonbonded interactions: 50280 Sorted by model distance: nonbonded pdb=" OD1 ASN A 476 " pdb=" NH1 ARG A 546 " model vdw 2.245 3.120 nonbonded pdb=" O ILE B 356 " pdb=" OG SER B 692 " model vdw 2.260 3.040 nonbonded pdb=" O ILE A 356 " pdb=" OG SER A 692 " model vdw 2.274 3.040 nonbonded pdb=" O VAL B 450 " pdb=" OG1 THR B 453 " model vdw 2.299 3.040 nonbonded pdb=" O VAL A 450 " pdb=" OG1 THR A 453 " model vdw 2.305 3.040 ... (remaining 50275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.660 Find NCS groups from input model: 0.200 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4670 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 : 0.003 0.061 6560 Z= 0.217 Angle : 0.702 7.266 8980 Z= 0.397 Chirality : 0.041 0.131 1094 Planarity : 0.007 0.098 1126 Dihedral : 12.332 81.117 2010 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.64 % 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: -0.47 (0.27), residues: 940 helix: 1.26 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.30 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 300 HIS 0.005 0.001 HIS B 695 PHE 0.021 0.001 PHE B 364 TYR 0.011 0.001 TYR A 533 ARG 0.008 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.615 Fit side-chains REVERT: A 428 MET cc_start: 0.4302 (tpp) cc_final: 0.3394 (ttp) REVERT: A 469 LYS cc_start: 0.6823 (mmmt) cc_final: 0.6396 (mmtt) REVERT: A 713 MET cc_start: 0.5462 (ptp) cc_final: 0.5207 (ptm) REVERT: B 428 MET cc_start: 0.4384 (tpp) cc_final: 0.3450 (ttp) REVERT: B 469 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6809 (mmtp) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1418 time to fit residues: 12.6426 Evaluate side-chains 45 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.0060 chunk 85 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.207091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.165753 restraints weight = 6966.196| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.53 r_work: 0.3842 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6560 Z= 0.218 Angle : 0.605 5.369 8980 Z= 0.317 Chirality : 0.042 0.132 1094 Planarity : 0.006 0.076 1126 Dihedral : 4.544 23.220 974 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.89 % Allowed : 10.50 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.27 (0.28), residues: 940 helix: 1.32 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -3.26 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 732 HIS 0.002 0.001 HIS A 695 PHE 0.015 0.002 PHE B 681 TYR 0.006 0.001 TYR A 533 ARG 0.003 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.758 Fit side-chains REVERT: A 428 MET cc_start: 0.4903 (tpp) cc_final: 0.3705 (ttp) REVERT: A 469 LYS cc_start: 0.7437 (mmmt) cc_final: 0.7145 (mmtp) REVERT: B 428 MET cc_start: 0.5268 (tpp) cc_final: 0.3972 (ttp) outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 0.1398 time to fit residues: 12.5628 Evaluate side-chains 48 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 0.0670 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.199076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157932 restraints weight = 7133.622| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.56 r_work: 0.3770 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6560 Z= 0.246 Angle : 0.597 5.095 8980 Z= 0.315 Chirality : 0.043 0.125 1094 Planarity : 0.005 0.066 1126 Dihedral : 4.554 21.490 974 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 1.96 % Allowed : 16.37 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.28), residues: 940 helix: 1.31 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.37 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 714 HIS 0.002 0.001 HIS A 695 PHE 0.015 0.002 PHE B 364 TYR 0.007 0.001 TYR A 584 ARG 0.003 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.614 Fit side-chains REVERT: A 428 MET cc_start: 0.5570 (tpp) cc_final: 0.4242 (ttp) REVERT: A 492 GLU cc_start: 0.7988 (tt0) cc_final: 0.7785 (tt0) REVERT: B 428 MET cc_start: 0.5503 (tpp) cc_final: 0.4207 (ttp) REVERT: B 492 GLU cc_start: 0.7973 (tt0) cc_final: 0.7684 (tt0) outliers start: 11 outliers final: 3 residues processed: 61 average time/residue: 0.1418 time to fit residues: 13.0333 Evaluate side-chains 48 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 697 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.200029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158575 restraints weight = 7097.821| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.58 r_work: 0.3783 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6560 Z= 0.204 Angle : 0.559 5.176 8980 Z= 0.293 Chirality : 0.041 0.122 1094 Planarity : 0.005 0.060 1126 Dihedral : 4.413 20.357 974 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.85 % Allowed : 16.55 % Favored : 80.60 % 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: -0.24 (0.28), residues: 940 helix: 1.42 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -3.37 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 430 HIS 0.001 0.000 HIS A 695 PHE 0.012 0.001 PHE A 364 TYR 0.004 0.001 TYR A 655 ARG 0.002 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.617 Fit side-chains REVERT: A 360 LEU cc_start: 0.5166 (OUTLIER) cc_final: 0.4937 (pp) REVERT: A 428 MET cc_start: 0.5355 (tpp) cc_final: 0.4127 (ttp) REVERT: A 468 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.4629 (m-80) REVERT: B 360 LEU cc_start: 0.4895 (OUTLIER) cc_final: 0.4684 (pp) REVERT: B 428 MET cc_start: 0.5347 (tpp) cc_final: 0.4057 (ttp) outliers start: 16 outliers final: 5 residues processed: 60 average time/residue: 0.1132 time to fit residues: 10.9333 Evaluate side-chains 51 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 697 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 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 = 0.4291 r_free = 0.4291 target = 0.196415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154710 restraints weight = 7108.375| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.56 r_work: 0.3744 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6560 Z= 0.254 Angle : 0.578 5.224 8980 Z= 0.304 Chirality : 0.042 0.124 1094 Planarity : 0.005 0.058 1126 Dihedral : 4.428 18.995 974 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.20 % Allowed : 18.33 % Favored : 78.47 % 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: -0.34 (0.28), residues: 940 helix: 1.33 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -3.36 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 714 HIS 0.001 0.001 HIS B 695 PHE 0.010 0.001 PHE A 488 TYR 0.007 0.001 TYR A 584 ARG 0.002 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.609 Fit side-chains REVERT: A 360 LEU cc_start: 0.5568 (OUTLIER) cc_final: 0.5320 (pp) REVERT: A 428 MET cc_start: 0.5579 (tpp) cc_final: 0.4323 (ttp) REVERT: B 360 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.5186 (pp) REVERT: B 428 MET cc_start: 0.5443 (tpp) cc_final: 0.4188 (ttp) REVERT: B 468 TYR cc_start: 0.5206 (OUTLIER) cc_final: 0.4550 (m-10) REVERT: B 499 THR cc_start: 0.8906 (p) cc_final: 0.8610 (p) outliers start: 18 outliers final: 9 residues processed: 64 average time/residue: 0.1260 time to fit residues: 12.3868 Evaluate side-chains 58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.196542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154658 restraints weight = 6994.993| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.55 r_work: 0.3748 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6560 Z= 0.237 Angle : 0.572 5.196 8980 Z= 0.300 Chirality : 0.041 0.126 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.400 18.112 974 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.74 % Allowed : 19.40 % Favored : 76.87 % 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: -0.23 (0.28), residues: 940 helix: 1.46 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -3.25 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 714 HIS 0.001 0.001 HIS A 695 PHE 0.011 0.001 PHE B 728 TYR 0.006 0.001 TYR B 711 ARG 0.002 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.641 Fit side-chains REVERT: A 360 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5756 (pp) REVERT: B 360 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5525 (pp) REVERT: B 468 TYR cc_start: 0.5220 (OUTLIER) cc_final: 0.4742 (m-80) REVERT: B 499 THR cc_start: 0.8811 (p) cc_final: 0.8484 (p) outliers start: 21 outliers final: 9 residues processed: 66 average time/residue: 0.1325 time to fit residues: 13.4032 Evaluate side-chains 58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 0.0980 chunk 64 optimal weight: 0.0170 chunk 13 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 82 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.199966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157946 restraints weight = 6912.209| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.56 r_work: 0.3779 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6560 Z= 0.176 Angle : 0.549 5.694 8980 Z= 0.284 Chirality : 0.040 0.148 1094 Planarity : 0.005 0.055 1126 Dihedral : 4.220 17.898 974 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.49 % Allowed : 21.17 % Favored : 76.33 % 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: 0.03 (0.28), residues: 940 helix: 1.62 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.18 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 732 HIS 0.000 0.000 HIS B 695 PHE 0.011 0.001 PHE A 488 TYR 0.005 0.001 TYR B 711 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.655 Fit side-chains REVERT: B 360 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5639 (pp) REVERT: B 454 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7206 (t80) REVERT: B 468 TYR cc_start: 0.5261 (OUTLIER) cc_final: 0.4599 (m-10) REVERT: B 499 THR cc_start: 0.8878 (p) cc_final: 0.8525 (p) REVERT: B 722 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6954 (tt) outliers start: 14 outliers final: 5 residues processed: 57 average time/residue: 0.1314 time to fit residues: 11.6899 Evaluate side-chains 51 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.197564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.155064 restraints weight = 7051.219| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.64 r_work: 0.3751 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6560 Z= 0.215 Angle : 0.570 7.284 8980 Z= 0.293 Chirality : 0.041 0.132 1094 Planarity : 0.005 0.056 1126 Dihedral : 4.246 17.101 974 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.85 % Allowed : 20.64 % Favored : 76.51 % 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: -0.03 (0.28), residues: 940 helix: 1.58 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.20 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.001 0.000 HIS B 695 PHE 0.011 0.001 PHE A 488 TYR 0.009 0.001 TYR A 739 ARG 0.002 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.608 Fit side-chains REVERT: B 360 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5863 (pp) REVERT: B 454 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7294 (t80) REVERT: B 468 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.4748 (m-10) REVERT: B 499 THR cc_start: 0.8829 (p) cc_final: 0.8482 (p) REVERT: B 722 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6918 (tt) outliers start: 16 outliers final: 8 residues processed: 59 average time/residue: 0.1413 time to fit residues: 12.5931 Evaluate side-chains 56 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 577 CYS Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 0.0170 chunk 87 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.202243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160432 restraints weight = 6915.702| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.57 r_work: 0.3810 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6560 Z= 0.160 Angle : 0.546 6.924 8980 Z= 0.278 Chirality : 0.040 0.121 1094 Planarity : 0.005 0.056 1126 Dihedral : 4.098 16.713 974 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.02 % Allowed : 21.00 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.28), residues: 940 helix: 1.75 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.20 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 430 HIS 0.000 0.000 HIS B 695 PHE 0.010 0.001 PHE A 488 TYR 0.005 0.001 TYR B 711 ARG 0.002 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.615 Fit side-chains REVERT: B 360 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5833 (pp) REVERT: B 468 TYR cc_start: 0.5181 (OUTLIER) cc_final: 0.4479 (m-10) REVERT: B 499 THR cc_start: 0.8813 (p) cc_final: 0.8446 (p) outliers start: 17 outliers final: 11 residues processed: 55 average time/residue: 0.1341 time to fit residues: 11.3535 Evaluate side-chains 53 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 577 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 73 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 86 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4641 r_free = 0.4641 target = 0.231961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190798 restraints weight = 7147.645| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.51 r_work: 0.4085 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6560 Z= 0.217 Angle : 0.573 6.891 8980 Z= 0.293 Chirality : 0.041 0.125 1094 Planarity : 0.005 0.056 1126 Dihedral : 4.159 16.081 974 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.96 % Allowed : 21.71 % Favored : 76.33 % 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: 0.02 (0.28), residues: 940 helix: 1.62 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.19 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 714 HIS 0.001 0.000 HIS B 695 PHE 0.012 0.001 PHE A 488 TYR 0.005 0.001 TYR B 584 ARG 0.002 0.000 ARG B 546 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.693 Fit side-chains REVERT: B 360 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6239 (pp) REVERT: B 468 TYR cc_start: 0.5404 (OUTLIER) cc_final: 0.4952 (m-10) REVERT: B 499 THR cc_start: 0.8894 (p) cc_final: 0.8545 (p) outliers start: 11 outliers final: 9 residues processed: 55 average time/residue: 0.1349 time to fit residues: 11.5315 Evaluate side-chains 57 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 577 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 65 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 = 0.4654 r_free = 0.4654 target = 0.233678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.191904 restraints weight = 7219.931| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.55 r_work: 0.4098 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6560 Z= 0.182 Angle : 0.557 6.831 8980 Z= 0.285 Chirality : 0.041 0.125 1094 Planarity : 0.005 0.056 1126 Dihedral : 4.112 16.094 974 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.14 % Allowed : 22.06 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.28), residues: 940 helix: 1.68 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.20 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 733 HIS 0.001 0.000 HIS B 695 PHE 0.009 0.001 PHE A 488 TYR 0.007 0.001 TYR A 739 ARG 0.001 0.000 ARG B 546 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2809.88 seconds wall clock time: 50 minutes 40.74 seconds (3040.74 seconds total)