Starting phenix.real_space_refine on Fri Dec 27 18:57:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s1z_24813/12_2024/7s1z_24813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s1z_24813/12_2024/7s1z_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_24813/12_2024/7s1z_24813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s1z_24813/12_2024/7s1z_24813.map" model { file = "/net/cci-nas-00/data/ceres_data/7s1z_24813/12_2024/7s1z_24813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s1z_24813/12_2024/7s1z_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-5532/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: 4.58, per 1000 atoms: 0.71 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: 1.56 Conformation dependent library (CDL) restraints added in 1.0 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: 0.54 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: 1.82 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: 0.00 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: 1.010 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: 0.060 Set scattering table: 0.070 Process input model: 18.340 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.620 ------------------------------------------------------------------------------- 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 : 0.651 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: 0.1354 time to fit residues: 12.0310 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 : 0.671 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4739 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 : 0.646 Fit side-chains REVERT: A 428 MET cc_start: 0.4323 (tpp) cc_final: 0.3471 (ttp) REVERT: A 469 LYS cc_start: 0.6797 (mmmt) cc_final: 0.6486 (mmtp) REVERT: B 428 MET cc_start: 0.4582 (tpp) cc_final: 0.3670 (ttp) outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 0.1307 time to fit residues: 11.8283 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 : 0.635 ------------------------------------------------------------------------------- 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 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 0.0070 chunk 68 optimal weight: 0.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4762 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6560 Z= 0.201 Angle : 0.570 5.249 8980 Z= 0.298 Chirality : 0.041 0.122 1094 Planarity : 0.005 0.064 1126 Dihedral : 4.429 21.597 974 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.14 % Allowed : 14.95 % Favored : 82.92 % 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: -0.12 (0.28), residues: 940 helix: 1.50 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -3.31 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 714 HIS 0.002 0.001 HIS A 695 PHE 0.012 0.001 PHE B 681 TYR 0.005 0.001 TYR B 655 ARG 0.002 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 57 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.681 Fit side-chains REVERT: A 428 MET cc_start: 0.4754 (tpp) cc_final: 0.3768 (ttp) REVERT: B 428 MET cc_start: 0.4945 (tpp) cc_final: 0.4007 (ttp) outliers start: 12 outliers final: 4 residues processed: 57 average time/residue: 0.1156 time to fit residues: 10.5356 Evaluate side-chains 45 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 697 SER 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 84 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4746 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6560 Z= 0.173 Angle : 0.541 5.225 8980 Z= 0.282 Chirality : 0.040 0.118 1094 Planarity : 0.005 0.058 1126 Dihedral : 4.285 20.696 974 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.31 % Allowed : 16.55 % Favored : 81.14 % 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: 0.05 (0.28), residues: 940 helix: 1.67 (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 0.008 0.001 TRP A 732 HIS 0.001 0.000 HIS A 695 PHE 0.009 0.001 PHE A 681 TYR 0.004 0.001 TYR A 655 ARG 0.002 0.000 ARG B 705 *********************** 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 55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.509 Fit side-chains REVERT: A 360 LEU cc_start: 0.2870 (OUTLIER) cc_final: 0.2630 (pp) REVERT: A 428 MET cc_start: 0.4847 (tpp) cc_final: 0.3868 (ttp) REVERT: A 468 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.3655 (m-10) REVERT: B 428 MET cc_start: 0.4896 (tpp) cc_final: 0.3968 (ttp) outliers start: 13 outliers final: 5 residues processed: 55 average time/residue: 0.1176 time to fit residues: 10.3843 Evaluate side-chains 48 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 697 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 22 optimal weight: 0.0470 chunk 30 optimal weight: 0.0030 overall best weight: 0.2486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4720 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6560 Z= 0.147 Angle : 0.524 5.312 8980 Z= 0.271 Chirality : 0.040 0.115 1094 Planarity : 0.005 0.055 1126 Dihedral : 4.096 20.024 974 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.49 % Allowed : 17.26 % Favored : 80.25 % 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: 0.21 (0.28), residues: 940 helix: 1.82 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.21 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 430 HIS 0.001 0.000 HIS B 695 PHE 0.007 0.001 PHE A 481 TYR 0.004 0.000 TYR A 746 ARG 0.002 0.000 ARG B 705 *********************** 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 56 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.704 Fit side-chains REVERT: A 360 LEU cc_start: 0.2817 (OUTLIER) cc_final: 0.2595 (pp) REVERT: A 468 TYR cc_start: 0.4243 (OUTLIER) cc_final: 0.3722 (m-10) outliers start: 14 outliers final: 4 residues processed: 56 average time/residue: 0.1218 time to fit residues: 11.3513 Evaluate side-chains 47 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 697 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4798 moved from start: 0.2663 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= 0.239 Angle : 0.564 5.303 8980 Z= 0.294 Chirality : 0.041 0.121 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.256 19.726 974 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.67 % Allowed : 17.97 % Favored : 79.36 % 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: -0.09 (0.28), residues: 940 helix: 1.62 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.27 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.001 0.000 HIS B 695 PHE 0.012 0.001 PHE B 728 TYR 0.005 0.001 TYR A 584 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 65 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.657 Fit side-chains REVERT: A 360 LEU cc_start: 0.3417 (OUTLIER) cc_final: 0.3176 (pp) REVERT: B 468 TYR cc_start: 0.4240 (OUTLIER) cc_final: 0.3605 (m-10) outliers start: 15 outliers final: 5 residues processed: 64 average time/residue: 0.1325 time to fit residues: 12.7838 Evaluate side-chains 55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 697 SER Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 697 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4811 moved from start: 0.2956 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= 0.232 Angle : 0.566 5.157 8980 Z= 0.295 Chirality : 0.041 0.130 1094 Planarity : 0.005 0.056 1126 Dihedral : 4.275 18.658 974 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.49 % Allowed : 18.68 % Favored : 78.83 % 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: 1.42 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -3.35 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 714 HIS 0.001 0.000 HIS A 695 PHE 0.013 0.001 PHE A 488 TYR 0.006 0.001 TYR B 584 ARG 0.002 0.000 ARG B 546 *********************** 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 63 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.663 Fit side-chains REVERT: A 360 LEU cc_start: 0.3762 (OUTLIER) cc_final: 0.3501 (pp) REVERT: B 468 TYR cc_start: 0.4263 (OUTLIER) cc_final: 0.3780 (m-10) REVERT: B 499 THR cc_start: 0.7310 (p) cc_final: 0.7030 (p) outliers start: 14 outliers final: 6 residues processed: 63 average time/residue: 0.1304 time to fit residues: 12.7951 Evaluate side-chains 55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 384 VAL Chi-restraints excluded: chain B residue 468 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4829 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6560 Z= 0.254 Angle : 0.583 5.521 8980 Z= 0.303 Chirality : 0.042 0.159 1094 Planarity : 0.005 0.056 1126 Dihedral : 4.325 17.786 974 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.49 % Allowed : 19.57 % Favored : 77.94 % 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: -0.18 (0.28), residues: 940 helix: 1.41 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -3.17 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 714 HIS 0.001 0.000 HIS A 695 PHE 0.012 0.001 PHE A 488 TYR 0.007 0.001 TYR A 584 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: 14 poor density : 47 time to evaluate : 0.622 Fit side-chains REVERT: A 360 LEU cc_start: 0.4255 (OUTLIER) cc_final: 0.3981 (pp) REVERT: B 499 THR cc_start: 0.7206 (p) cc_final: 0.6917 (p) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.1282 time to fit residues: 11.8564 Evaluate side-chains 56 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4808 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6560 Z= 0.209 Angle : 0.568 5.724 8980 Z= 0.293 Chirality : 0.041 0.133 1094 Planarity : 0.005 0.055 1126 Dihedral : 4.242 17.194 974 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.60 % Allowed : 21.00 % Favored : 77.40 % 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: -0.08 (0.28), residues: 940 helix: 1.53 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.21 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 430 HIS 0.001 0.000 HIS A 695 PHE 0.012 0.001 PHE A 488 TYR 0.008 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 53 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 1.120 Fit side-chains REVERT: A 360 LEU cc_start: 0.4502 (OUTLIER) cc_final: 0.4225 (pp) REVERT: B 499 THR cc_start: 0.7130 (p) cc_final: 0.6834 (p) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.1347 time to fit residues: 10.7805 Evaluate side-chains 53 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL 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 42 optimal weight: 0.0870 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 86 optimal weight: 0.0770 chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4781 moved from start: 0.3218 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 5.992 8980 Z= 0.281 Chirality : 0.040 0.127 1094 Planarity : 0.005 0.054 1126 Dihedral : 4.072 16.392 974 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.07 % Allowed : 21.89 % Favored : 77.05 % 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: 0.08 (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 732 HIS 0.001 0.000 HIS A 695 PHE 0.011 0.001 PHE A 488 TYR 0.005 0.001 TYR B 711 ARG 0.001 0.000 ARG B 705 ********************** 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 50 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.670 Fit side-chains REVERT: A 360 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.4255 (pp) REVERT: B 499 THR cc_start: 0.7335 (p) cc_final: 0.7058 (p) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.1353 time to fit residues: 10.0827 Evaluate side-chains 50 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 577 CYS Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 384 VAL 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 68 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4647 r_free = 0.4647 target = 0.232843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.191644 restraints weight = 7102.966| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.51 r_work: 0.4095 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.3290 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= 0.207 Angle : 0.562 5.647 8980 Z= 0.288 Chirality : 0.041 0.130 1094 Planarity : 0.005 0.055 1126 Dihedral : 4.114 16.145 974 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 1.42 % Allowed : 21.17 % Favored : 77.40 % 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: 0.06 (0.28), residues: 940 helix: 1.66 (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 A 695 PHE 0.012 0.001 PHE A 488 TYR 0.005 0.001 TYR B 711 ARG 0.002 0.000 ARG B 546 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1407.59 seconds wall clock time: 26 minutes 29.47 seconds (1589.47 seconds total)