Starting phenix.real_space_refine on Thu Mar 6 08:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k12_36784/03_2025/8k12_36784_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k12_36784/03_2025/8k12_36784.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/8k12_36784/03_2025/8k12_36784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k12_36784/03_2025/8k12_36784.map" model { file = "/net/cci-nas-00/data/ceres_data/8k12_36784/03_2025/8k12_36784_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k12_36784/03_2025/8k12_36784_neut.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= -0.000 sd= 0.046 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 48 5.16 5 C 3730 2.51 5 N 872 2.21 5 O 942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 5592 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2796 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 349} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2796 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 349} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 4.23, per 1000 atoms: 0.76 Number of scatterers: 5592 At special positions: 0 Unit cell: (99.22, 71.34, 77.08, 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 48 16.00 O 942 8.00 N 872 7.00 C 3730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 787 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 787 " 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: 1.37 Conformation dependent library (CDL) restraints added in 611.1 milliseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1348 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 80.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 289 through 317 removed outlier: 3.991A pdb=" N TYR A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 479 removed outlier: 3.554A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.620A pdb=" N ILE A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.836A pdb=" N ILE A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 removed outlier: 3.709A pdb=" N GLY A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 596 removed outlier: 3.671A pdb=" N PHE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N MET A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 625 Processing helix chain 'A' and resid 630 through 652 removed outlier: 4.128A pdb=" N SER A 638 " --> pdb=" O TRP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 713 through 740 removed outlier: 3.562A pdb=" N LEU A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 734 " --> pdb=" O PHE A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 767 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 794 through 816 removed outlier: 3.666A pdb=" N ILE A 805 " --> pdb=" O PHE A 801 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 317 removed outlier: 3.996A pdb=" N TYR B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 479 removed outlier: 3.554A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix Processing helix chain 'B' and resid 499 through 505 removed outlier: 3.620A pdb=" N ILE B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.835A pdb=" N ILE B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 removed outlier: 3.709A pdb=" N GLY B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS B 568 " --> pdb=" O SER B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 596 removed outlier: 3.670A pdb=" N PHE B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N MET B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 625 Processing helix chain 'B' and resid 630 through 652 removed outlier: 4.128A pdb=" N SER B 638 " --> pdb=" O TRP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 Processing helix chain 'B' and resid 713 through 740 removed outlier: 3.562A pdb=" N LEU B 719 " --> pdb=" O ALA B 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 734 " --> pdb=" O PHE B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 767 removed outlier: 3.501A pdb=" N PHE B 761 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 794 through 816 removed outlier: 3.666A pdb=" N ILE B 805 " --> pdb=" O PHE B 801 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 814 " --> pdb=" O SER B 810 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1257 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: 1.47 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1678 1.35 - 1.46: 1456 1.46 - 1.58: 2522 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 5728 Sorted by residual: bond pdb=" N THR B 289 " pdb=" CA THR B 289 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.52e+00 bond pdb=" N THR A 289 " pdb=" CA THR A 289 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.32e+00 bond pdb=" N ILE B 586 " pdb=" CA ILE B 586 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.19e-02 7.06e+03 6.39e+00 bond pdb=" N ILE A 586 " pdb=" CA ILE A 586 " ideal model delta sigma weight residual 1.461 1.490 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N LEU B 592 " pdb=" CA LEU B 592 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.72e+00 ... (remaining 5723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7212 1.21 - 2.42: 430 2.42 - 3.64: 114 3.64 - 4.85: 30 4.85 - 6.06: 10 Bond angle restraints: 7796 Sorted by residual: angle pdb=" C SER A 295 " pdb=" N GLY A 296 " pdb=" CA GLY A 296 " ideal model delta sigma weight residual 119.98 124.36 -4.38 1.11e+00 8.12e-01 1.56e+01 angle pdb=" C SER B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta sigma weight residual 119.98 124.34 -4.36 1.11e+00 8.12e-01 1.55e+01 angle pdb=" C LEU A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta sigma weight residual 119.98 124.33 -4.35 1.11e+00 8.12e-01 1.54e+01 angle pdb=" C LEU B 301 " pdb=" N GLY B 302 " pdb=" CA GLY B 302 " ideal model delta sigma weight residual 119.98 124.21 -4.23 1.11e+00 8.12e-01 1.45e+01 angle pdb=" N GLN A 596 " pdb=" CA GLN A 596 " pdb=" C GLN A 596 " ideal model delta sigma weight residual 113.20 109.19 4.01 1.21e+00 6.83e-01 1.10e+01 ... (remaining 7791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 2875 16.04 - 32.07: 297 32.07 - 48.11: 80 48.11 - 64.15: 20 64.15 - 80.18: 4 Dihedral angle restraints: 3276 sinusoidal: 1196 harmonic: 2080 Sorted by residual: dihedral pdb=" CA PHE A 576 " pdb=" C PHE A 576 " pdb=" N GLN A 577 " pdb=" CA GLN A 577 " ideal model delta harmonic sigma weight residual -180.00 -151.93 -28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA PHE B 576 " pdb=" C PHE B 576 " pdb=" N GLN B 577 " pdb=" CA GLN B 577 " ideal model delta harmonic sigma weight residual 180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA MET B 559 " pdb=" C MET B 559 " pdb=" N GLU B 560 " pdb=" CA GLU B 560 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 3273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 660 0.042 - 0.085: 192 0.085 - 0.127: 43 0.127 - 0.169: 29 0.169 - 0.212: 10 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA ILE B 586 " pdb=" N ILE B 586 " pdb=" C ILE B 586 " pdb=" CB ILE B 586 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE A 586 " pdb=" N ILE A 586 " pdb=" C ILE A 586 " pdb=" CB ILE A 586 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR A 311 " pdb=" CA THR A 311 " pdb=" OG1 THR A 311 " pdb=" CG2 THR A 311 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 931 not shown) Planarity restraints: 942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 308 " 0.070 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR A 308 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 308 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 308 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 308 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 308 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 308 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 308 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 308 " -0.070 2.00e-02 2.50e+03 4.39e-02 3.85e+01 pdb=" CG TYR B 308 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 308 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 308 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR B 308 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR B 308 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 308 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 308 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 304 " 0.040 2.00e-02 2.50e+03 2.56e-02 1.14e+01 pdb=" CG PHE A 304 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 304 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 304 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 304 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 304 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 304 " 0.031 2.00e-02 2.50e+03 ... (remaining 939 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 580 2.75 - 3.29: 6039 3.29 - 3.82: 9252 3.82 - 4.36: 10919 4.36 - 4.90: 17906 Nonbonded interactions: 44696 Sorted by model distance: nonbonded pdb=" OH TYR A 293 " pdb=" O PRO A 493 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR A 486 " pdb=" O VAL A 569 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR B 486 " pdb=" O VAL B 569 " model vdw 2.228 3.040 nonbonded pdb=" O ASN B 501 " pdb=" OG SER B 505 " model vdw 2.262 3.040 nonbonded pdb=" O ASN A 501 " pdb=" OG SER A 505 " model vdw 2.263 3.040 ... (remaining 44691 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: 2.170 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.210 Find NCS groups from input model: 0.100 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.005 0.036 5728 Z= 0.305 Angle : 0.710 6.061 7796 Z= 0.470 Chirality : 0.050 0.212 934 Planarity : 0.004 0.044 942 Dihedral : 14.817 80.183 1916 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.50 % Allowed : 16.22 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.31), residues: 694 helix: 1.47 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.48 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 317 HIS 0.002 0.001 HIS B 492 PHE 0.040 0.002 PHE A 304 TYR 0.078 0.004 TYR A 308 ARG 0.001 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 286 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LEU cc_start: 0.7758 (mt) cc_final: 0.7508 (mt) REVERT: A 562 LEU cc_start: 0.6917 (tt) cc_final: 0.6697 (tt) REVERT: A 791 ASP cc_start: 0.7372 (m-30) cc_final: 0.7104 (t0) REVERT: A 794 ASP cc_start: 0.6138 (p0) cc_final: 0.5749 (p0) REVERT: B 308 TYR cc_start: 0.8073 (m-80) cc_final: 0.6944 (m-80) REVERT: B 462 LEU cc_start: 0.7815 (mt) cc_final: 0.7584 (mt) REVERT: B 562 LEU cc_start: 0.6933 (tt) cc_final: 0.6708 (tt) REVERT: B 791 ASP cc_start: 0.7429 (m-30) cc_final: 0.7043 (t0) REVERT: B 794 ASP cc_start: 0.6038 (p0) cc_final: 0.5748 (p0) outliers start: 3 outliers final: 0 residues processed: 286 average time/residue: 0.1393 time to fit residues: 53.3133 Evaluate side-chains 172 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN A 527 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS B 526 ASN B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.167295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.136597 restraints weight = 11477.459| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 3.54 r_work: 0.3895 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5728 Z= 0.223 Angle : 0.708 11.224 7796 Z= 0.357 Chirality : 0.042 0.149 934 Planarity : 0.004 0.027 942 Dihedral : 4.364 28.025 748 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.68 % Allowed : 24.25 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.30), residues: 694 helix: 1.88 (0.20), residues: 548 sheet: None (None), residues: 0 loop : -1.54 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 700 HIS 0.008 0.001 HIS B 527 PHE 0.043 0.003 PHE B 811 TYR 0.022 0.002 TYR B 717 ARG 0.002 0.000 ARG B 785 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.8096 (m-80) cc_final: 0.7666 (m-80) REVERT: A 462 LEU cc_start: 0.8510 (mt) cc_final: 0.8301 (mt) REVERT: A 472 GLN cc_start: 0.8833 (tp40) cc_final: 0.8567 (tp40) REVERT: A 791 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7278 (t0) REVERT: B 308 TYR cc_start: 0.8058 (m-80) cc_final: 0.7662 (m-80) REVERT: B 472 GLN cc_start: 0.8880 (tp40) cc_final: 0.8657 (tp40) REVERT: B 612 CYS cc_start: 0.9069 (t) cc_final: 0.8678 (p) REVERT: B 709 MET cc_start: 0.7843 (tpp) cc_final: 0.7467 (tpp) REVERT: B 791 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7202 (t0) outliers start: 16 outliers final: 7 residues processed: 195 average time/residue: 0.1348 time to fit residues: 36.0452 Evaluate side-chains 174 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 HIS B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.163971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.133490 restraints weight = 11769.776| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.52 r_work: 0.3879 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5728 Z= 0.216 Angle : 0.619 8.532 7796 Z= 0.317 Chirality : 0.039 0.154 934 Planarity : 0.003 0.026 942 Dihedral : 4.330 23.724 748 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.01 % Allowed : 24.41 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.30), residues: 694 helix: 2.03 (0.20), residues: 548 sheet: None (None), residues: 0 loop : -1.67 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 700 HIS 0.008 0.001 HIS A 527 PHE 0.023 0.002 PHE A 761 TYR 0.009 0.001 TYR B 486 ARG 0.001 0.000 ARG B 785 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 PHE cc_start: 0.3047 (OUTLIER) cc_final: 0.2186 (t80) REVERT: A 462 LEU cc_start: 0.8466 (mt) cc_final: 0.8204 (mt) REVERT: A 472 GLN cc_start: 0.8845 (tp40) cc_final: 0.8497 (tp40) REVERT: A 637 PHE cc_start: 0.8525 (t80) cc_final: 0.8314 (m-80) REVERT: A 791 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7251 (t0) REVERT: A 807 MET cc_start: 0.8039 (tpp) cc_final: 0.7828 (tpp) REVERT: B 308 TYR cc_start: 0.8118 (m-80) cc_final: 0.7715 (m-80) REVERT: B 450 PHE cc_start: 0.2780 (OUTLIER) cc_final: 0.1858 (t80) REVERT: B 472 GLN cc_start: 0.8886 (tp40) cc_final: 0.8617 (tp40) REVERT: B 637 PHE cc_start: 0.8482 (t80) cc_final: 0.8251 (m-80) REVERT: B 709 MET cc_start: 0.7859 (tpp) cc_final: 0.7445 (tpp) REVERT: B 791 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7165 (t0) outliers start: 24 outliers final: 12 residues processed: 190 average time/residue: 0.1242 time to fit residues: 33.0926 Evaluate side-chains 177 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 821 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 0.0370 chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS A 796 HIS B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.162584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.131885 restraints weight = 12142.664| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 3.56 r_work: 0.3859 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5728 Z= 0.207 Angle : 0.638 12.611 7796 Z= 0.311 Chirality : 0.039 0.165 934 Planarity : 0.003 0.026 942 Dihedral : 4.315 23.508 748 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.52 % Allowed : 24.75 % Favored : 69.73 % 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: 2.06 (0.30), residues: 694 helix: 2.09 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -1.59 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 700 HIS 0.004 0.001 HIS A 527 PHE 0.021 0.002 PHE A 811 TYR 0.008 0.001 TYR B 486 ARG 0.001 0.000 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 PHE cc_start: 0.3233 (OUTLIER) cc_final: 0.2363 (t80) REVERT: A 462 LEU cc_start: 0.8463 (mt) cc_final: 0.8204 (mt) REVERT: A 472 GLN cc_start: 0.8805 (tp40) cc_final: 0.8460 (tp40) REVERT: A 791 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7289 (t0) REVERT: B 308 TYR cc_start: 0.8117 (m-80) cc_final: 0.7704 (m-80) REVERT: B 450 PHE cc_start: 0.3089 (OUTLIER) cc_final: 0.2175 (t80) REVERT: B 472 GLN cc_start: 0.8844 (tp40) cc_final: 0.8545 (tp40) REVERT: B 709 MET cc_start: 0.7891 (tpp) cc_final: 0.7436 (tpp) REVERT: B 791 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7243 (t0) outliers start: 33 outliers final: 13 residues processed: 185 average time/residue: 0.1353 time to fit residues: 34.6976 Evaluate side-chains 174 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 759 TRP Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 805 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 0.0980 chunk 35 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.164471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.134437 restraints weight = 11819.790| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.43 r_work: 0.3932 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5728 Z= 0.177 Angle : 0.613 10.877 7796 Z= 0.301 Chirality : 0.038 0.149 934 Planarity : 0.003 0.026 942 Dihedral : 4.297 23.174 748 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.85 % Allowed : 26.42 % Favored : 69.73 % 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: 2.08 (0.30), residues: 694 helix: 2.10 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -1.60 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 700 HIS 0.012 0.001 HIS A 527 PHE 0.028 0.002 PHE A 811 TYR 0.010 0.001 TYR A 573 ARG 0.001 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.8128 (m-80) cc_final: 0.7841 (m-10) REVERT: A 450 PHE cc_start: 0.3484 (OUTLIER) cc_final: 0.2597 (t80) REVERT: A 462 LEU cc_start: 0.8410 (mt) cc_final: 0.8133 (mt) REVERT: A 472 GLN cc_start: 0.8613 (tp40) cc_final: 0.8366 (tp40) REVERT: A 775 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7893 (mmmt) REVERT: A 791 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7323 (t0) REVERT: B 472 GLN cc_start: 0.8666 (tp40) cc_final: 0.8418 (tp40) REVERT: B 709 MET cc_start: 0.7856 (tpp) cc_final: 0.7380 (tpp) REVERT: B 775 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7889 (mmmt) REVERT: B 791 ASP cc_start: 0.8253 (m-30) cc_final: 0.7316 (t0) outliers start: 23 outliers final: 9 residues processed: 179 average time/residue: 0.1617 time to fit residues: 40.7462 Evaluate side-chains 168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 759 TRP Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 775 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.162891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.132528 restraints weight = 11927.667| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.59 r_work: 0.3870 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5728 Z= 0.192 Angle : 0.621 13.470 7796 Z= 0.306 Chirality : 0.038 0.159 934 Planarity : 0.003 0.026 942 Dihedral : 4.290 23.035 748 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.68 % Allowed : 26.76 % Favored : 68.56 % 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: 2.16 (0.31), residues: 694 helix: 2.17 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -1.60 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 799 HIS 0.007 0.001 HIS B 527 PHE 0.031 0.002 PHE A 732 TYR 0.007 0.001 TYR A 573 ARG 0.001 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 PHE cc_start: 0.3601 (OUTLIER) cc_final: 0.2719 (t80) REVERT: A 462 LEU cc_start: 0.8394 (mt) cc_final: 0.8135 (mt) REVERT: A 472 GLN cc_start: 0.8772 (tp40) cc_final: 0.8395 (tp40) REVERT: A 514 LEU cc_start: 0.8822 (tt) cc_final: 0.8611 (tp) REVERT: A 736 MET cc_start: 0.7950 (ptp) cc_final: 0.7711 (ptp) REVERT: A 775 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7892 (mmmt) REVERT: A 791 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7317 (t0) REVERT: B 450 PHE cc_start: 0.3367 (OUTLIER) cc_final: 0.2460 (t80) REVERT: B 472 GLN cc_start: 0.8793 (tp40) cc_final: 0.8445 (tp40) REVERT: B 709 MET cc_start: 0.7889 (tpp) cc_final: 0.7385 (tpp) REVERT: B 775 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7947 (mmmt) REVERT: B 791 ASP cc_start: 0.8267 (m-30) cc_final: 0.7237 (t0) outliers start: 28 outliers final: 16 residues processed: 177 average time/residue: 0.1280 time to fit residues: 31.1651 Evaluate side-chains 168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 759 TRP Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.163528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.134087 restraints weight = 11882.889| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.51 r_work: 0.3881 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5728 Z= 0.188 Angle : 0.659 12.930 7796 Z= 0.320 Chirality : 0.039 0.170 934 Planarity : 0.003 0.026 942 Dihedral : 4.339 23.196 748 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.18 % Allowed : 28.26 % Favored : 68.56 % 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: 2.18 (0.31), residues: 694 helix: 2.16 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.33 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 799 HIS 0.012 0.001 HIS B 527 PHE 0.013 0.001 PHE B 811 TYR 0.025 0.001 TYR B 573 ARG 0.001 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 PHE cc_start: 0.3542 (OUTLIER) cc_final: 0.2650 (t80) REVERT: A 472 GLN cc_start: 0.8783 (tp40) cc_final: 0.8355 (tp40) REVERT: A 736 MET cc_start: 0.8031 (ptp) cc_final: 0.7799 (ptp) REVERT: A 791 ASP cc_start: 0.8280 (m-30) cc_final: 0.7285 (t0) REVERT: B 450 PHE cc_start: 0.3501 (OUTLIER) cc_final: 0.2613 (t80) REVERT: B 472 GLN cc_start: 0.8856 (tp40) cc_final: 0.8491 (tp40) REVERT: B 709 MET cc_start: 0.7885 (tpp) cc_final: 0.7391 (tpp) REVERT: B 775 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7931 (mmmt) REVERT: B 791 ASP cc_start: 0.8272 (m-30) cc_final: 0.7214 (t0) outliers start: 19 outliers final: 14 residues processed: 171 average time/residue: 0.1299 time to fit residues: 30.8293 Evaluate side-chains 166 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 759 TRP Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.160296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.130470 restraints weight = 11964.645| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.52 r_work: 0.3841 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5728 Z= 0.269 Angle : 0.687 11.170 7796 Z= 0.340 Chirality : 0.041 0.172 934 Planarity : 0.003 0.024 942 Dihedral : 4.362 22.575 748 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.35 % Allowed : 28.09 % Favored : 67.56 % 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: 2.14 (0.31), residues: 694 helix: 2.12 (0.20), residues: 544 sheet: None (None), residues: 0 loop : -1.26 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 799 HIS 0.012 0.002 HIS B 527 PHE 0.052 0.003 PHE B 618 TYR 0.020 0.001 TYR B 573 ARG 0.002 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 PHE cc_start: 0.3858 (OUTLIER) cc_final: 0.3080 (t80) REVERT: A 472 GLN cc_start: 0.8822 (tp40) cc_final: 0.8375 (tp40) REVERT: A 710 ARG cc_start: 0.7363 (mtt180) cc_final: 0.6679 (mtp-110) REVERT: A 736 MET cc_start: 0.8099 (ptp) cc_final: 0.7883 (ptp) REVERT: A 791 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7334 (t0) REVERT: B 450 PHE cc_start: 0.3797 (OUTLIER) cc_final: 0.2966 (t80) REVERT: B 472 GLN cc_start: 0.8859 (tp40) cc_final: 0.8524 (tp40) REVERT: B 709 MET cc_start: 0.7973 (tpp) cc_final: 0.7432 (tpp) REVERT: B 710 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6667 (mtp-110) REVERT: B 775 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7994 (mmmt) REVERT: B 791 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7257 (t0) outliers start: 26 outliers final: 16 residues processed: 165 average time/residue: 0.1406 time to fit residues: 31.7238 Evaluate side-chains 165 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 TRP Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.158896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.129184 restraints weight = 11963.654| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.45 r_work: 0.3858 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5728 Z= 0.283 Angle : 0.720 11.410 7796 Z= 0.358 Chirality : 0.042 0.175 934 Planarity : 0.003 0.025 942 Dihedral : 4.481 22.938 748 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.18 % Allowed : 28.09 % Favored : 67.73 % 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: 2.01 (0.31), residues: 694 helix: 1.99 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.16 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 799 HIS 0.012 0.002 HIS B 527 PHE 0.040 0.002 PHE B 618 TYR 0.016 0.001 TYR B 573 ARG 0.002 0.000 ARG B 529 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 GLN cc_start: 0.8836 (tp40) cc_final: 0.8402 (tp40) REVERT: A 710 ARG cc_start: 0.7580 (mtt180) cc_final: 0.6760 (mtm110) REVERT: A 736 MET cc_start: 0.8087 (ptp) cc_final: 0.7880 (ptp) REVERT: A 791 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7358 (t0) REVERT: A 794 ASP cc_start: 0.8043 (t70) cc_final: 0.7601 (m-30) REVERT: B 472 GLN cc_start: 0.8843 (tp40) cc_final: 0.8495 (tp40) REVERT: B 710 ARG cc_start: 0.7564 (mtt180) cc_final: 0.6772 (mtp-110) REVERT: B 775 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.7991 (mmmt) REVERT: B 791 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7297 (t0) outliers start: 25 outliers final: 19 residues processed: 166 average time/residue: 0.1389 time to fit residues: 31.6185 Evaluate side-chains 172 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 759 TRP Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.161508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.132580 restraints weight = 12055.678| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.48 r_work: 0.3855 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5728 Z= 0.182 Angle : 0.696 11.106 7796 Z= 0.347 Chirality : 0.040 0.176 934 Planarity : 0.003 0.026 942 Dihedral : 4.401 22.477 748 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.68 % Allowed : 29.26 % Favored : 67.06 % 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: 2.14 (0.31), residues: 694 helix: 2.09 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.13 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 799 HIS 0.012 0.002 HIS A 527 PHE 0.037 0.002 PHE B 618 TYR 0.009 0.001 TYR A 717 ARG 0.001 0.000 ARG A 785 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 GLN cc_start: 0.8821 (tp40) cc_final: 0.8361 (tp40) REVERT: A 710 ARG cc_start: 0.7493 (mtt180) cc_final: 0.6684 (mtm110) REVERT: A 791 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7321 (t0) REVERT: A 794 ASP cc_start: 0.7898 (t70) cc_final: 0.7416 (m-30) REVERT: B 472 GLN cc_start: 0.8832 (tp40) cc_final: 0.8473 (tp40) REVERT: B 709 MET cc_start: 0.7883 (tpp) cc_final: 0.7418 (tpp) REVERT: B 710 ARG cc_start: 0.7472 (mtt180) cc_final: 0.6650 (mtp-110) REVERT: B 732 PHE cc_start: 0.8708 (m-80) cc_final: 0.8475 (m-80) REVERT: B 775 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7947 (mmmt) REVERT: B 791 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7269 (t0) REVERT: B 794 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7357 (m-30) outliers start: 22 outliers final: 14 residues processed: 161 average time/residue: 0.1303 time to fit residues: 28.7186 Evaluate side-chains 164 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 612 CYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 794 ASP Chi-restraints excluded: chain B residue 815 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 0.0570 chunk 41 optimal weight: 0.0070 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.163049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.134486 restraints weight = 12047.702| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.45 r_work: 0.3909 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5728 Z= 0.171 Angle : 0.687 10.830 7796 Z= 0.338 Chirality : 0.040 0.172 934 Planarity : 0.003 0.027 942 Dihedral : 4.353 22.052 748 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.68 % Allowed : 28.76 % Favored : 67.56 % 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: 2.17 (0.31), residues: 694 helix: 2.10 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.14 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 799 HIS 0.013 0.001 HIS B 527 PHE 0.036 0.002 PHE B 618 TYR 0.009 0.001 TYR A 486 ARG 0.001 0.000 ARG A 785 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.86 seconds wall clock time: 55 minutes 37.85 seconds (3337.85 seconds total)