Starting phenix.real_space_refine on Thu Nov 14 09:54:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k12_36784/11_2024/8k12_36784_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k12_36784/11_2024/8k12_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k12_36784/11_2024/8k12_36784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k12_36784/11_2024/8k12_36784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k12_36784/11_2024/8k12_36784_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k12_36784/11_2024/8k12_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-5513/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: 4.39, per 1000 atoms: 0.79 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: 1.46 Conformation dependent library (CDL) restraints added in 672.5 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: 0.47 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: 1.57 Time building geometry restraints manager: 1.69 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.410 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.380 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- 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 : 0.566 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: 0.1439 time to fit residues: 54.8125 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 : 0.605 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.7956 (m-80) cc_final: 0.7661 (m-80) REVERT: A 791 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7073 (t0) REVERT: B 308 TYR cc_start: 0.7924 (m-80) cc_final: 0.7625 (m-80) REVERT: B 626 PHE cc_start: 0.6019 (m-80) cc_final: 0.5769 (m-80) REVERT: B 773 TRP cc_start: 0.4084 (OUTLIER) cc_final: 0.3645 (p90) REVERT: B 791 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6998 (t0) outliers start: 16 outliers final: 7 residues processed: 195 average time/residue: 0.1375 time to fit residues: 36.3769 Evaluate side-chains 174 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 773 TRP 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 35 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 0.0470 chunk 17 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5728 Z= 0.195 Angle : 0.622 8.878 7796 Z= 0.318 Chirality : 0.039 0.156 934 Planarity : 0.003 0.027 942 Dihedral : 4.359 23.674 748 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.85 % Allowed : 23.91 % Favored : 72.24 % 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: 1.87 (0.30), residues: 694 helix: 1.98 (0.20), residues: 548 sheet: None (None), residues: 0 loop : -1.69 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 700 HIS 0.008 0.001 HIS A 527 PHE 0.022 0.002 PHE A 761 TYR 0.009 0.001 TYR A 471 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 203 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.7966 (m-80) cc_final: 0.7668 (m-80) REVERT: A 791 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7049 (t0) REVERT: B 308 TYR cc_start: 0.7928 (m-80) cc_final: 0.7635 (m-80) REVERT: B 626 PHE cc_start: 0.5927 (m-80) cc_final: 0.5719 (m-80) REVERT: B 791 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6935 (t0) outliers start: 23 outliers final: 13 residues processed: 195 average time/residue: 0.1283 time to fit residues: 34.6998 Evaluate side-chains 175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 VAL 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 458 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 773 TRP 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 47 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS B 476 ASN B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4605 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= 0.187 Angle : 0.637 12.652 7796 Z= 0.311 Chirality : 0.039 0.169 934 Planarity : 0.003 0.026 942 Dihedral : 4.332 23.539 748 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.69 % Allowed : 24.58 % 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: 1.97 (0.30), residues: 694 helix: 2.04 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -1.72 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 700 HIS 0.004 0.001 HIS A 527 PHE 0.024 0.002 PHE A 811 TYR 0.009 0.001 TYR B 717 ARG 0.001 0.000 ARG A 785 *********************** 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 205 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.7966 (m-80) cc_final: 0.7744 (m-80) REVERT: A 450 PHE cc_start: 0.3463 (OUTLIER) cc_final: 0.2356 (t80) REVERT: A 791 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7060 (t0) REVERT: B 450 PHE cc_start: 0.3178 (OUTLIER) cc_final: 0.1960 (t80) REVERT: B 736 MET cc_start: 0.7885 (mpp) cc_final: 0.7564 (ptp) REVERT: B 791 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6927 (t0) outliers start: 34 outliers final: 13 residues processed: 185 average time/residue: 0.1272 time to fit residues: 32.7990 Evaluate side-chains 169 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 562 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 736 MET 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 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 773 TRP 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 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5728 Z= 0.367 Angle : 0.717 12.527 7796 Z= 0.361 Chirality : 0.043 0.164 934 Planarity : 0.003 0.028 942 Dihedral : 4.528 23.108 748 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: 1.74 (0.30), residues: 694 helix: 1.82 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -1.46 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 700 HIS 0.012 0.002 HIS A 527 PHE 0.025 0.003 PHE A 811 TYR 0.016 0.002 TYR A 573 ARG 0.003 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 186 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 PHE cc_start: 0.4166 (OUTLIER) cc_final: 0.3234 (t80) REVERT: A 710 ARG cc_start: 0.6687 (mtt180) cc_final: 0.6366 (mtp-110) REVERT: A 791 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7142 (t0) REVERT: B 450 PHE cc_start: 0.3990 (OUTLIER) cc_final: 0.2971 (t80) REVERT: B 710 ARG cc_start: 0.6710 (mtt180) cc_final: 0.6390 (mtp-110) REVERT: B 791 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7114 (t0) REVERT: B 811 PHE cc_start: 0.7807 (m-80) cc_final: 0.7586 (m-80) outliers start: 33 outliers final: 16 residues processed: 173 average time/residue: 0.1479 time to fit residues: 34.3163 Evaluate side-chains 163 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER 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 294 VAL Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 467 LEU 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 791 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** B 527 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5728 Z= 0.234 Angle : 0.638 10.992 7796 Z= 0.320 Chirality : 0.040 0.182 934 Planarity : 0.003 0.023 942 Dihedral : 4.405 23.708 748 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.02 % Allowed : 26.25 % Favored : 68.73 % 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 (0.31), residues: 694 helix: 2.07 (0.20), residues: 546 sheet: None (None), residues: 0 loop : -1.33 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 799 HIS 0.006 0.001 HIS B 527 PHE 0.029 0.002 PHE A 732 TYR 0.009 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 183 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 TYR cc_start: 0.8328 (m-80) cc_final: 0.7820 (m-10) REVERT: A 514 LEU cc_start: 0.8339 (tt) cc_final: 0.8112 (tt) REVERT: A 710 ARG cc_start: 0.6550 (mtt180) cc_final: 0.6247 (mtp-110) REVERT: A 791 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7129 (t0) REVERT: B 450 PHE cc_start: 0.4386 (OUTLIER) cc_final: 0.3477 (t80) REVERT: B 710 ARG cc_start: 0.6682 (mtt180) cc_final: 0.6291 (mtm110) REVERT: B 791 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7042 (t0) REVERT: B 811 PHE cc_start: 0.7790 (m-80) cc_final: 0.7551 (m-80) outliers start: 30 outliers final: 13 residues processed: 169 average time/residue: 0.1410 time to fit residues: 32.2195 Evaluate side-chains 161 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER 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 B residue 450 PHE Chi-restraints excluded: chain B residue 498 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 773 TRP Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 805 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 0.0270 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 0.0010 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5244 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5728 Z= 0.183 Angle : 0.657 10.465 7796 Z= 0.334 Chirality : 0.040 0.168 934 Planarity : 0.003 0.025 942 Dihedral : 4.413 23.331 748 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.51 % Allowed : 28.09 % Favored : 68.39 % 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: 2.09 (0.31), residues: 694 helix: 2.08 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.32 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 799 HIS 0.012 0.001 HIS B 527 PHE 0.048 0.002 PHE A 618 TYR 0.010 0.001 TYR B 717 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 170 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 710 ARG cc_start: 0.6508 (mtt180) cc_final: 0.6192 (mtp-110) REVERT: A 791 ASP cc_start: 0.7353 (m-30) cc_final: 0.7093 (t0) REVERT: B 710 ARG cc_start: 0.6535 (mtt180) cc_final: 0.6206 (mtp-110) REVERT: B 791 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7062 (t0) outliers start: 21 outliers final: 11 residues processed: 161 average time/residue: 0.1427 time to fit residues: 31.3291 Evaluate side-chains 155 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 791 ASP 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 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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** B 783 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5728 Z= 0.206 Angle : 0.694 13.027 7796 Z= 0.344 Chirality : 0.041 0.172 934 Planarity : 0.003 0.024 942 Dihedral : 4.413 22.794 748 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.18 % Allowed : 29.10 % 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: 2.12 (0.31), residues: 694 helix: 2.08 (0.20), residues: 546 sheet: None (None), residues: 0 loop : -1.23 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 799 HIS 0.007 0.001 HIS A 527 PHE 0.039 0.002 PHE B 618 TYR 0.026 0.001 TYR B 573 ARG 0.002 0.000 ARG A 781 *********************** 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 166 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 710 ARG cc_start: 0.6515 (mtt180) cc_final: 0.6208 (mtp-110) REVERT: A 791 ASP cc_start: 0.7381 (m-30) cc_final: 0.7081 (t0) REVERT: B 585 MET cc_start: 0.7314 (ptp) cc_final: 0.7027 (ptp) REVERT: B 710 ARG cc_start: 0.6508 (mtt180) cc_final: 0.6216 (mtp-110) REVERT: B 791 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7068 (t0) outliers start: 19 outliers final: 12 residues processed: 158 average time/residue: 0.1442 time to fit residues: 30.9809 Evaluate side-chains 160 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 498 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 717 TYR Chi-restraints excluded: chain B residue 773 TRP Chi-restraints excluded: chain B residue 791 ASP 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 27 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5728 Z= 0.258 Angle : 0.725 12.227 7796 Z= 0.361 Chirality : 0.041 0.176 934 Planarity : 0.003 0.024 942 Dihedral : 4.492 22.840 748 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.18 % Allowed : 30.10 % Favored : 66.72 % 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: 2.14 (0.31), residues: 694 helix: 2.08 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.16 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 799 HIS 0.012 0.002 HIS B 527 PHE 0.045 0.003 PHE A 732 TYR 0.025 0.001 TYR B 573 ARG 0.001 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 164 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 710 ARG cc_start: 0.6648 (mtt180) cc_final: 0.6325 (mtp-110) REVERT: A 791 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7117 (t0) REVERT: B 585 MET cc_start: 0.7412 (ptp) cc_final: 0.7059 (ptp) REVERT: B 710 ARG cc_start: 0.6621 (mtt180) cc_final: 0.6303 (mtp-110) REVERT: B 791 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7105 (t0) outliers start: 19 outliers final: 14 residues processed: 156 average time/residue: 0.1478 time to fit residues: 31.5313 Evaluate side-chains 155 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER 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 815 LEU Chi-restraints excluded: chain B residue 498 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 717 TYR Chi-restraints excluded: chain B residue 773 TRP 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 69 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5774 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= 0.204 Angle : 0.717 12.434 7796 Z= 0.362 Chirality : 0.041 0.175 934 Planarity : 0.003 0.026 942 Dihedral : 4.510 22.624 748 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.51 % Allowed : 30.43 % 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: 2.07 (0.31), residues: 694 helix: 2.01 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.10 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 799 HIS 0.012 0.001 HIS B 527 PHE 0.046 0.002 PHE B 732 TYR 0.011 0.001 TYR B 573 ARG 0.002 0.000 ARG A 781 ********************** 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 160 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 710 ARG cc_start: 0.6530 (mtt180) cc_final: 0.6292 (mtp-110) REVERT: B 585 MET cc_start: 0.7398 (ptp) cc_final: 0.7067 (ptp) REVERT: B 710 ARG cc_start: 0.6505 (mtt180) cc_final: 0.6207 (mtp-110) REVERT: B 732 PHE cc_start: 0.7748 (m-80) cc_final: 0.7535 (m-80) REVERT: B 791 ASP cc_start: 0.7280 (m-30) cc_final: 0.7079 (t0) outliers start: 15 outliers final: 13 residues processed: 154 average time/residue: 0.1417 time to fit residues: 29.7563 Evaluate side-chains 153 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 717 TYR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 717 TYR Chi-restraints excluded: chain B residue 773 TRP 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 15 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 0.0870 chunk 7 optimal weight: 0.0370 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.0060 chunk 37 optimal weight: 3.9990 overall best weight: 0.2652 ------------------------------------------------------------------------------- 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 472 GLN B 527 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.168235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.141240 restraints weight = 11584.174| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.34 r_work: 0.3894 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5728 Z= 0.187 Angle : 0.702 11.999 7796 Z= 0.351 Chirality : 0.040 0.169 934 Planarity : 0.003 0.026 942 Dihedral : 4.386 22.077 748 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.68 % Allowed : 29.60 % 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: 2.12 (0.31), residues: 694 helix: 2.06 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.12 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 799 HIS 0.013 0.001 HIS B 527 PHE 0.049 0.002 PHE B 732 TYR 0.011 0.001 TYR B 573 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: 1553.33 seconds wall clock time: 28 minutes 51.74 seconds (1731.74 seconds total)