Starting phenix.real_space_refine on Tue Mar 11 17:58:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s1z_24813/03_2025/7s1z_24813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s1z_24813/03_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_24813/03_2025/7s1z_24813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s1z_24813/03_2025/7s1z_24813.map" model { file = "/net/cci-nas-00/data/ceres_data/7s1z_24813/03_2025/7s1z_24813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s1z_24813/03_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-5624/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: 4.85, per 1000 atoms: 0.76 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: 1.78 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: 2.09 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: 0.860 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: 19.730 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- 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 : 0.619 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: 0.1405 time to fit residues: 12.7474 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 : 0.586 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.165732 restraints weight = 6966.196| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.54 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: 0.6349 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 : 0.592 Fit side-chains REVERT: A 428 MET cc_start: 0.4906 (tpp) cc_final: 0.3709 (ttp) REVERT: A 469 LYS cc_start: 0.7434 (mmmt) cc_final: 0.7141 (mmtp) REVERT: B 428 MET cc_start: 0.5269 (tpp) cc_final: 0.3974 (ttp) outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 0.1315 time to fit residues: 11.8832 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 : 0.571 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 80 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 30 optimal weight: 0.0060 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.207112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166044 restraints weight = 6995.461| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.56 r_work: 0.3845 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.1612 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= 0.179 Angle : 0.557 5.230 8980 Z= 0.290 Chirality : 0.041 0.187 1094 Planarity : 0.005 0.062 1126 Dihedral : 4.391 21.880 974 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.31 % Allowed : 14.41 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -3.27 (0.32), residues: 330 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 0.010 0.001 PHE A 681 TYR 0.003 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 54 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.593 Fit side-chains REVERT: A 428 MET cc_start: 0.5321 (tpp) cc_final: 0.4031 (ttp) REVERT: B 428 MET cc_start: 0.5330 (tpp) cc_final: 0.4064 (ttp) REVERT: B 492 GLU cc_start: 0.7889 (tt0) cc_final: 0.7639 (tt0) outliers start: 13 outliers final: 4 residues processed: 53 average time/residue: 0.1198 time to fit residues: 10.0110 Evaluate side-chains 44 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.0770 chunk 7 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 0.0060 overall best weight: 0.2354 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.209180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.167569 restraints weight = 7042.939| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.67 r_work: 0.3872 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6560 Z= 0.146 Angle : 0.529 5.292 8980 Z= 0.274 Chirality : 0.040 0.115 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.191 21.053 974 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.31 % Allowed : 14.95 % Favored : 82.74 % 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: 0.19 (0.28), residues: 940 helix: 1.81 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.20 (0.30), residues: 340 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 0.009 0.001 PHE B 364 TYR 0.003 0.000 TYR A 746 ARG 0.002 0.001 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 52 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.575 Fit side-chains REVERT: A 360 LEU cc_start: 0.4306 (OUTLIER) cc_final: 0.4101 (pp) REVERT: A 428 MET cc_start: 0.5291 (tpp) cc_final: 0.4112 (ttm) REVERT: B 428 MET cc_start: 0.5335 (tpp) cc_final: 0.4230 (ttm) outliers start: 13 outliers final: 5 residues processed: 52 average time/residue: 0.1164 time to fit residues: 9.7433 Evaluate side-chains 44 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 697 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.200635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.159143 restraints weight = 7129.188| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.58 r_work: 0.3785 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6560 Z= 0.222 Angle : 0.560 5.103 8980 Z= 0.293 Chirality : 0.041 0.124 1094 Planarity : 0.005 0.057 1126 Dihedral : 4.264 20.547 974 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.67 % Allowed : 16.90 % Favored : 80.43 % 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: -0.10 (0.28), residues: 940 helix: 1.61 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.26 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 714 HIS 0.002 0.001 HIS B 695 PHE 0.012 0.002 PHE A 364 TYR 0.006 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 63 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.646 Fit side-chains REVERT: A 428 MET cc_start: 0.5462 (tpp) cc_final: 0.4280 (ttm) REVERT: B 428 MET cc_start: 0.5557 (tpp) cc_final: 0.4302 (ttp) outliers start: 15 outliers final: 5 residues processed: 62 average time/residue: 0.1214 time to fit residues: 12.0607 Evaluate side-chains 51 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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 73 optimal weight: 7.9990 chunk 53 optimal weight: 0.0770 chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.201794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.160443 restraints weight = 6952.707| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.56 r_work: 0.3807 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2548 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= 0.188 Angle : 0.551 6.159 8980 Z= 0.283 Chirality : 0.040 0.114 1094 Planarity : 0.005 0.056 1126 Dihedral : 4.221 19.972 974 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.31 % Allowed : 17.97 % Favored : 79.72 % 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: 1.65 (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 733 HIS 0.001 0.000 HIS B 695 PHE 0.007 0.001 PHE B 488 TYR 0.010 0.001 TYR A 739 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 59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.595 Fit side-chains REVERT: B 468 TYR cc_start: 0.5074 (OUTLIER) cc_final: 0.3996 (m-10) REVERT: B 722 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6886 (tt) outliers start: 13 outliers final: 5 residues processed: 59 average time/residue: 0.1123 time to fit residues: 10.6758 Evaluate side-chains 54 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 468 TYR Chi-restraints excluded: chain B residue 697 SER 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: 0.3980 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 23 optimal weight: 0.0050 chunk 4 optimal weight: 0.6980 chunk 82 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.204633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.163172 restraints weight = 6926.968| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.56 r_work: 0.3836 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.2678 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= 0.161 Angle : 0.539 5.282 8980 Z= 0.275 Chirality : 0.040 0.113 1094 Planarity : 0.005 0.055 1126 Dihedral : 4.081 19.337 974 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.60 % Allowed : 18.68 % Favored : 79.72 % 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: 0.15 (0.28), residues: 940 helix: 1.76 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.20 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 704 HIS 0.001 0.000 HIS A 695 PHE 0.009 0.001 PHE A 488 TYR 0.009 0.001 TYR A 711 ARG 0.001 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 56 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.674 Fit side-chains REVERT: B 468 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4083 (m-10) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.1215 time to fit residues: 10.9072 Evaluate side-chains 51 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 468 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 7 optimal weight: 0.1980 chunk 36 optimal weight: 30.0000 chunk 79 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 18 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.204297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.162105 restraints weight = 7038.386| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.64 r_work: 0.3828 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.2803 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= 0.166 Angle : 0.534 5.198 8980 Z= 0.272 Chirality : 0.040 0.115 1094 Planarity : 0.005 0.055 1126 Dihedral : 4.033 19.072 974 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 1.25 % Allowed : 19.93 % 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: 0.19 (0.28), residues: 940 helix: 1.80 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.19 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 714 HIS 0.001 0.000 HIS B 695 PHE 0.009 0.001 PHE A 488 TYR 0.004 0.000 TYR A 711 ARG 0.001 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 52 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.645 Fit side-chains REVERT: B 468 TYR cc_start: 0.5074 (OUTLIER) cc_final: 0.4073 (m-10) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.1332 time to fit residues: 10.7167 Evaluate side-chains 50 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 468 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 74 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.206128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.164499 restraints weight = 7000.073| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.56 r_work: 0.3851 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6560 Z= 0.156 Angle : 0.535 5.660 8980 Z= 0.271 Chirality : 0.040 0.114 1094 Planarity : 0.005 0.055 1126 Dihedral : 3.978 18.884 974 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.07 % Allowed : 20.46 % 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: 0.26 (0.28), residues: 940 helix: 1.84 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.14 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 733 HIS 0.001 0.000 HIS B 695 PHE 0.008 0.001 PHE A 488 TYR 0.004 0.000 TYR A 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 51 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.655 Fit side-chains REVERT: B 296 MET cc_start: 0.5804 (ttm) cc_final: 0.5575 (ttp) REVERT: B 468 TYR cc_start: 0.5085 (OUTLIER) cc_final: 0.4077 (m-10) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.1395 time to fit residues: 10.8964 Evaluate side-chains 49 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 343 THR Chi-restraints excluded: chain B residue 468 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 7 optimal weight: 0.1980 chunk 86 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.203608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.161598 restraints weight = 7038.944| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.59 r_work: 0.3816 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.3012 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= 0.181 Angle : 0.543 5.829 8980 Z= 0.276 Chirality : 0.040 0.116 1094 Planarity : 0.005 0.055 1126 Dihedral : 3.995 18.448 974 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.89 % Allowed : 21.17 % 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: 0.25 (0.28), residues: 940 helix: 1.83 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.12 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 714 HIS 0.001 0.000 HIS A 695 PHE 0.010 0.001 PHE A 488 TYR 0.004 0.001 TYR B 584 ARG 0.001 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 50 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.636 Fit side-chains REVERT: B 468 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.4361 (m-10) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.1353 time to fit residues: 10.4275 Evaluate side-chains 50 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 343 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 468 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 82 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.200534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158133 restraints weight = 7129.039| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.58 r_work: 0.3783 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6560 Z= 0.208 Angle : 0.559 5.991 8980 Z= 0.286 Chirality : 0.041 0.125 1094 Planarity : 0.005 0.055 1126 Dihedral : 4.085 18.120 974 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.42 % Allowed : 21.00 % Favored : 77.58 % 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: 0.15 (0.28), residues: 940 helix: 1.72 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.10 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 655 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: 2807.46 seconds wall clock time: 49 minutes 12.93 seconds (2952.93 seconds total)