Starting phenix.real_space_refine on Mon Sep 23 23:04:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/09_2024/8q74_18203.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/09_2024/8q74_18203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/09_2024/8q74_18203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/09_2024/8q74_18203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/09_2024/8q74_18203.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q74_18203/09_2024/8q74_18203.cif" } resolution = 3.68 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= 0.023 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: 5 Type Number sf(0) Gaussians Cu 1 5.60 5 S 34 5.16 5 C 3812 2.51 5 N 988 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5943 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5942 Classifications: {'peptide': 783} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 745} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3243 SG CYS A 597 27.486 24.901 48.334 1.00140.08 S ATOM 3256 SG CYS A 599 28.127 29.237 48.453 1.00142.78 S Time building chain proxies: 4.27, per 1000 atoms: 0.72 Number of scatterers: 5943 At special positions: 0 Unit cell: (80.408, 86.3328, 141.349, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 1 28.99 S 34 16.00 O 1108 8.00 N 988 7.00 C 3812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 amino acid link not found "ATOM 1377 SD MET A 352 .*. S " "ATOM 3256 SG CYS A 599 .*. S " Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 875.3 milliseconds 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 53.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 197 through 209 removed outlier: 4.285A pdb=" N ARG A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.599A pdb=" N ALA A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 296 removed outlier: 3.793A pdb=" N PHE A 286 " --> pdb=" O TRP A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 300 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 317 through 332 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 335 through 348 removed outlier: 6.499A pdb=" N ALA A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 377 removed outlier: 3.696A pdb=" N LEU A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 420 removed outlier: 4.094A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 531 removed outlier: 3.635A pdb=" N GLN A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 546 through 567 removed outlier: 3.520A pdb=" N TRP A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.638A pdb=" N LEU A 593 " --> pdb=" O GLY A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 618 removed outlier: 4.010A pdb=" N MET A 610 " --> pdb=" O PRO A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 Processing helix chain 'A' and resid 682 through 693 removed outlier: 4.373A pdb=" N THR A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.825A pdb=" N GLU A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 768 Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 804 through 816 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 869 through 876 removed outlier: 3.900A pdb=" N ILE A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 875 " --> pdb=" O VAL A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 922 removed outlier: 4.123A pdb=" N ILE A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 915 " --> pdb=" O GLY A 911 " (cutoff:3.500A) Proline residue: A 918 - end of helix Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 933 through 954 removed outlier: 4.146A pdb=" N ALA A 939 " --> pdb=" O TRP A 935 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 941 " --> pdb=" O ALA A 937 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 954 " --> pdb=" O CYS A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 958 Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 312 removed outlier: 3.628A pdb=" N VAL A 311 " --> pdb=" O MET A 315 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N MET A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 425 Processing sheet with id=AA3, first strand: chain 'A' and resid 454 through 455 removed outlier: 4.082A pdb=" N CYS A 504 " --> pdb=" O GLN A 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 820 through 821 removed outlier: 8.929A pdb=" N PHE A 821 " --> pdb=" O SER A 797 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET A 799 " --> pdb=" O PHE A 821 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A 637 " --> pdb=" O ALA A 844 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 831 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: 1.87 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1893 1.34 - 1.46: 801 1.46 - 1.57: 3309 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6057 Sorted by residual: bond pdb=" CA CYS A 597 " pdb=" C CYS A 597 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.26e-02 6.30e+03 1.59e+01 bond pdb=" CA CYS A 599 " pdb=" C CYS A 599 " ideal model delta sigma weight residual 1.527 1.495 0.032 1.30e-02 5.92e+03 5.93e+00 bond pdb=" CA MET A 352 " pdb=" C MET A 352 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.28e-02 6.10e+03 4.59e+00 bond pdb=" N ALA A 600 " pdb=" CA ALA A 600 " ideal model delta sigma weight residual 1.458 1.433 0.026 1.26e-02 6.30e+03 4.14e+00 bond pdb=" CA ASP A 353 " pdb=" C ASP A 353 " ideal model delta sigma weight residual 1.525 1.499 0.026 1.37e-02 5.33e+03 3.62e+00 ... (remaining 6052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 7903 2.42 - 4.85: 279 4.85 - 7.27: 38 7.27 - 9.69: 4 9.69 - 12.12: 2 Bond angle restraints: 8226 Sorted by residual: angle pdb=" N ALA A 600 " pdb=" CA ALA A 600 " pdb=" C ALA A 600 " ideal model delta sigma weight residual 111.69 103.10 8.59 1.23e+00 6.61e-01 4.88e+01 angle pdb=" C THR A 656 " pdb=" N LYS A 657 " pdb=" CA LYS A 657 " ideal model delta sigma weight residual 122.11 112.10 10.01 1.59e+00 3.96e-01 3.97e+01 angle pdb=" N VAL A 311 " pdb=" CA VAL A 311 " pdb=" C VAL A 311 " ideal model delta sigma weight residual 113.53 108.53 5.00 9.80e-01 1.04e+00 2.60e+01 angle pdb=" C LYS A 657 " pdb=" N VAL A 658 " pdb=" CA VAL A 658 " ideal model delta sigma weight residual 120.13 128.17 -8.04 1.58e+00 4.01e-01 2.59e+01 angle pdb=" N TRP A 335 " pdb=" CA TRP A 335 " pdb=" C TRP A 335 " ideal model delta sigma weight residual 113.43 107.54 5.89 1.26e+00 6.30e-01 2.18e+01 ... (remaining 8221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3320 17.59 - 35.18: 277 35.18 - 52.77: 34 52.77 - 70.36: 13 70.36 - 87.95: 8 Dihedral angle restraints: 3652 sinusoidal: 1403 harmonic: 2249 Sorted by residual: dihedral pdb=" CA PRO A 250 " pdb=" C PRO A 250 " pdb=" N PRO A 251 " pdb=" CA PRO A 251 " ideal model delta harmonic sigma weight residual 180.00 139.23 40.77 0 5.00e+00 4.00e-02 6.65e+01 dihedral pdb=" CA ASN A 721 " pdb=" C ASN A 721 " pdb=" N VAL A 722 " pdb=" CA VAL A 722 " ideal model delta harmonic sigma weight residual 180.00 -144.73 -35.27 0 5.00e+00 4.00e-02 4.98e+01 dihedral pdb=" CA GLY A 724 " pdb=" C GLY A 724 " pdb=" N LYS A 725 " pdb=" CA LYS A 725 " ideal model delta harmonic sigma weight residual 180.00 -153.04 -26.96 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 3649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 705 0.048 - 0.096: 209 0.096 - 0.144: 50 0.144 - 0.192: 8 0.192 - 0.240: 2 Chirality restraints: 974 Sorted by residual: chirality pdb=" CB ILE A 704 " pdb=" CA ILE A 704 " pdb=" CG1 ILE A 704 " pdb=" CG2 ILE A 704 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA THR A 656 " pdb=" N THR A 656 " pdb=" C THR A 656 " pdb=" CB THR A 656 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CB ILE A 662 " pdb=" CA ILE A 662 " pdb=" CG1 ILE A 662 " pdb=" CG2 ILE A 662 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 971 not shown) Planarity restraints: 1041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 662 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO A 663 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 663 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 663 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 570 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO A 571 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 740 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO A 741 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 741 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 741 " 0.036 5.00e-02 4.00e+02 ... (remaining 1038 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 11 2.29 - 2.94: 2791 2.94 - 3.59: 9756 3.59 - 4.25: 14043 4.25 - 4.90: 22453 Nonbonded interactions: 49054 Sorted by model distance: nonbonded pdb=" CE MET A 352 " pdb="CU CU A1001 " model vdw 1.633 2.660 nonbonded pdb=" SG CYS A 597 " pdb="CU CU A1001 " model vdw 2.079 2.600 nonbonded pdb=" SD MET A 352 " pdb="CU CU A1001 " model vdw 2.087 2.600 nonbonded pdb=" O VAL A 687 " pdb=" OG1 THR A 690 " model vdw 2.178 3.040 nonbonded pdb=" OE1 GLU A 476 " pdb=" N MET A 478 " model vdw 2.183 3.120 ... (remaining 49049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.510 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.170 Find NCS groups from input model: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.004 0.071 6057 Z= 0.291 Angle : 1.020 12.117 8226 Z= 0.613 Chirality : 0.048 0.240 974 Planarity : 0.008 0.077 1041 Dihedral : 14.005 87.951 2204 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.90 % Allowed : 15.88 % Favored : 83.23 % Rotamer: Outliers : 0.15 % Allowed : 1.23 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 2.78 % Twisted General : 0.13 % 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: -2.37 (0.30), residues: 781 helix: 0.65 (0.28), residues: 366 sheet: -3.40 (0.73), residues: 30 loop : -3.90 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 558 HIS 0.009 0.001 HIS A 473 PHE 0.020 0.002 PHE A 582 TYR 0.028 0.002 TYR A 689 ARG 0.008 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 PHE cc_start: 0.9357 (m-80) cc_final: 0.9065 (m-80) REVERT: A 315 MET cc_start: 0.9055 (ppp) cc_final: 0.8799 (tmm) REVERT: A 319 MET cc_start: 0.8325 (mpp) cc_final: 0.8016 (mtp) REVERT: A 331 PHE cc_start: 0.7861 (m-80) cc_final: 0.7285 (m-80) REVERT: A 686 ILE cc_start: 0.9548 (mt) cc_final: 0.9235 (mt) REVERT: A 790 LEU cc_start: 0.9583 (mt) cc_final: 0.9329 (pp) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1550 time to fit residues: 17.0400 Evaluate side-chains 46 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 32 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.0010 overall best weight: 0.8966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 448 GLN ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6057 Z= 0.240 Angle : 0.848 9.330 8226 Z= 0.437 Chirality : 0.047 0.176 974 Planarity : 0.006 0.066 1041 Dihedral : 6.507 38.672 826 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.24 % Favored : 83.99 % Rotamer: Outliers : 1.23 % Allowed : 10.17 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 2.78 % Twisted General : 0.13 % 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: -1.86 (0.31), residues: 781 helix: 0.92 (0.27), residues: 383 sheet: -3.03 (0.76), residues: 31 loop : -3.67 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 558 HIS 0.012 0.002 HIS A 473 PHE 0.029 0.002 PHE A 293 TYR 0.017 0.002 TYR A 253 ARG 0.006 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 TRP cc_start: 0.8185 (m100) cc_final: 0.7981 (m-10) REVERT: A 315 MET cc_start: 0.9104 (ppp) cc_final: 0.8831 (tmm) REVERT: A 319 MET cc_start: 0.8404 (mpp) cc_final: 0.8126 (mpp) REVERT: A 601 LEU cc_start: 0.9170 (mm) cc_final: 0.8870 (mm) REVERT: A 689 TYR cc_start: 0.8960 (p90) cc_final: 0.8610 (p90) REVERT: A 799 MET cc_start: 0.8994 (ppp) cc_final: 0.8419 (ppp) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.1308 time to fit residues: 11.8825 Evaluate side-chains 50 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 19 optimal weight: 0.0980 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 53 optimal weight: 0.0060 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6057 Z= 0.210 Angle : 0.777 8.605 8226 Z= 0.401 Chirality : 0.046 0.244 974 Planarity : 0.006 0.062 1041 Dihedral : 6.253 35.534 826 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.77 % Allowed : 13.70 % Favored : 85.53 % Rotamer: Outliers : 2.62 % Allowed : 13.87 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 2.78 % Twisted General : 0.13 % 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: -1.61 (0.30), residues: 781 helix: 1.04 (0.27), residues: 394 sheet: -2.18 (0.86), residues: 21 loop : -3.63 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.024 0.002 PHE A 331 TYR 0.013 0.001 TYR A 689 ARG 0.004 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 MET cc_start: 0.8449 (mpp) cc_final: 0.8158 (mpp) REVERT: A 331 PHE cc_start: 0.8770 (m-80) cc_final: 0.8378 (m-80) REVERT: A 689 TYR cc_start: 0.8998 (p90) cc_final: 0.8573 (p90) REVERT: A 799 MET cc_start: 0.8938 (ppp) cc_final: 0.8553 (ppp) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 0.1311 time to fit residues: 13.1229 Evaluate side-chains 56 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6057 Z= 0.190 Angle : 0.742 11.434 8226 Z= 0.378 Chirality : 0.045 0.175 974 Planarity : 0.005 0.061 1041 Dihedral : 6.099 38.080 826 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.77 % Allowed : 13.44 % Favored : 85.79 % Rotamer: Outliers : 2.62 % Allowed : 13.87 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 2.78 % Twisted General : 0.13 % 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: -1.36 (0.31), residues: 781 helix: 1.32 (0.27), residues: 395 sheet: -1.97 (0.87), residues: 21 loop : -3.62 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.011 0.001 PHE A 710 TYR 0.023 0.001 TYR A 689 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.9501 (t80) cc_final: 0.9258 (t80) REVERT: A 315 MET cc_start: 0.9261 (tmm) cc_final: 0.9011 (tmm) REVERT: A 319 MET cc_start: 0.8391 (mpp) cc_final: 0.8143 (mpp) REVERT: A 331 PHE cc_start: 0.8766 (m-80) cc_final: 0.8435 (m-80) REVERT: A 689 TYR cc_start: 0.9014 (p90) cc_final: 0.8544 (p90) REVERT: A 705 MET cc_start: 0.8737 (ppp) cc_final: 0.8505 (ppp) REVERT: A 799 MET cc_start: 0.8899 (ppp) cc_final: 0.8642 (tmm) REVERT: A 845 MET cc_start: 0.8466 (ppp) cc_final: 0.7881 (ptm) REVERT: A 881 MET cc_start: 0.9187 (tpp) cc_final: 0.8986 (tmm) outliers start: 17 outliers final: 10 residues processed: 61 average time/residue: 0.1439 time to fit residues: 12.8564 Evaluate side-chains 55 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 6057 Z= 0.561 Angle : 0.942 11.061 8226 Z= 0.492 Chirality : 0.049 0.165 974 Planarity : 0.006 0.060 1041 Dihedral : 6.332 38.491 826 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.77 % Allowed : 14.72 % Favored : 84.51 % Rotamer: Outliers : 4.47 % Allowed : 16.18 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.98 (0.29), residues: 781 helix: 0.66 (0.25), residues: 381 sheet: -2.04 (1.11), residues: 23 loop : -3.59 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 908 HIS 0.011 0.002 HIS A 473 PHE 0.033 0.003 PHE A 395 TYR 0.023 0.003 TYR A 253 ARG 0.006 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 38 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.9442 (t80) cc_final: 0.9120 (t80) REVERT: A 319 MET cc_start: 0.8545 (mpp) cc_final: 0.8220 (mpp) REVERT: A 331 PHE cc_start: 0.8952 (m-80) cc_final: 0.8388 (m-80) REVERT: A 689 TYR cc_start: 0.9314 (p90) cc_final: 0.8866 (p90) REVERT: A 705 MET cc_start: 0.8796 (ppp) cc_final: 0.8230 (ppp) REVERT: A 799 MET cc_start: 0.8969 (ppp) cc_final: 0.8700 (tmm) outliers start: 29 outliers final: 22 residues processed: 62 average time/residue: 0.1545 time to fit residues: 13.5728 Evaluate side-chains 58 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 36 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 949 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 40.0000 chunk 24 optimal weight: 40.0000 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6057 Z= 0.201 Angle : 0.750 10.934 8226 Z= 0.385 Chirality : 0.046 0.152 974 Planarity : 0.005 0.061 1041 Dihedral : 6.156 38.381 826 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.68 % Favored : 86.43 % Rotamer: Outliers : 3.24 % Allowed : 18.64 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.51 (0.30), residues: 781 helix: 1.18 (0.26), residues: 397 sheet: -2.22 (0.90), residues: 21 loop : -3.69 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.011 0.002 PHE A 280 TYR 0.019 0.001 TYR A 689 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.9456 (t80) cc_final: 0.9114 (t80) REVERT: A 315 MET cc_start: 0.9278 (tmm) cc_final: 0.8985 (tmm) REVERT: A 331 PHE cc_start: 0.8877 (m-80) cc_final: 0.8408 (m-80) REVERT: A 689 TYR cc_start: 0.9165 (p90) cc_final: 0.8724 (p90) REVERT: A 705 MET cc_start: 0.8803 (ppp) cc_final: 0.8481 (ppp) REVERT: A 799 MET cc_start: 0.8959 (ppp) cc_final: 0.8704 (tmm) REVERT: A 845 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7888 (ptp) outliers start: 21 outliers final: 14 residues processed: 63 average time/residue: 0.1397 time to fit residues: 12.8532 Evaluate side-chains 58 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0020 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 40.0000 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6057 Z= 0.209 Angle : 0.750 11.723 8226 Z= 0.381 Chirality : 0.045 0.144 974 Planarity : 0.005 0.058 1041 Dihedral : 5.950 38.782 826 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.29 % Favored : 86.81 % Rotamer: Outliers : 3.08 % Allowed : 19.11 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.41 (0.31), residues: 781 helix: 1.34 (0.26), residues: 394 sheet: -2.64 (0.85), residues: 33 loop : -3.69 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.011 0.001 PHE A 303 TYR 0.017 0.001 TYR A 689 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.9512 (t80) cc_final: 0.9293 (t80) REVERT: A 315 MET cc_start: 0.9251 (tmm) cc_final: 0.8951 (tmm) REVERT: A 331 PHE cc_start: 0.8866 (m-80) cc_final: 0.8423 (m-80) REVERT: A 689 TYR cc_start: 0.9230 (p90) cc_final: 0.8813 (p90) REVERT: A 705 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8466 (ppp) REVERT: A 799 MET cc_start: 0.8975 (ppp) cc_final: 0.8712 (tmm) REVERT: A 845 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7778 (ptp) outliers start: 20 outliers final: 14 residues processed: 60 average time/residue: 0.1420 time to fit residues: 12.5528 Evaluate side-chains 59 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6057 Z= 0.196 Angle : 0.749 10.276 8226 Z= 0.377 Chirality : 0.046 0.277 974 Planarity : 0.005 0.068 1041 Dihedral : 5.867 38.945 826 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.78 % Favored : 87.32 % Rotamer: Outliers : 2.00 % Allowed : 19.72 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.36 (0.31), residues: 781 helix: 1.45 (0.27), residues: 393 sheet: -2.72 (0.70), residues: 41 loop : -3.72 (0.29), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.012 0.001 PHE A 291 TYR 0.018 0.001 TYR A 689 ARG 0.001 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.9807 (mmtm) cc_final: 0.9342 (tppt) REVERT: A 315 MET cc_start: 0.9258 (tmm) cc_final: 0.8871 (tmm) REVERT: A 319 MET cc_start: 0.8067 (mtp) cc_final: 0.7450 (tmm) REVERT: A 331 PHE cc_start: 0.8901 (m-80) cc_final: 0.8541 (m-80) REVERT: A 689 TYR cc_start: 0.9195 (p90) cc_final: 0.8738 (p90) REVERT: A 705 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8511 (ppp) REVERT: A 799 MET cc_start: 0.8977 (ppp) cc_final: 0.8720 (tmm) REVERT: A 845 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7851 (ptp) outliers start: 13 outliers final: 7 residues processed: 56 average time/residue: 0.1495 time to fit residues: 12.0721 Evaluate side-chains 58 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 50.0000 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 66 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 74 optimal weight: 0.0010 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6057 Z= 0.186 Angle : 0.753 11.228 8226 Z= 0.383 Chirality : 0.045 0.327 974 Planarity : 0.005 0.073 1041 Dihedral : 5.719 39.029 826 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.65 % Favored : 87.45 % Rotamer: Outliers : 2.00 % Allowed : 19.72 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 781 helix: 1.43 (0.27), residues: 393 sheet: -2.35 (0.83), residues: 23 loop : -3.54 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.011 0.001 PHE A 659 TYR 0.018 0.001 TYR A 689 ARG 0.005 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.9801 (mmtm) cc_final: 0.9332 (tppt) REVERT: A 315 MET cc_start: 0.9240 (tmm) cc_final: 0.8846 (tmm) REVERT: A 319 MET cc_start: 0.7976 (mtp) cc_final: 0.7413 (tmm) REVERT: A 331 PHE cc_start: 0.8888 (m-80) cc_final: 0.8462 (m-80) REVERT: A 689 TYR cc_start: 0.9231 (p90) cc_final: 0.8788 (p90) REVERT: A 705 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8435 (ppp) REVERT: A 799 MET cc_start: 0.8988 (ppp) cc_final: 0.8727 (tmm) REVERT: A 845 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7855 (ptp) outliers start: 13 outliers final: 8 residues processed: 56 average time/residue: 0.1574 time to fit residues: 12.6284 Evaluate side-chains 58 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN A 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6057 Z= 0.232 Angle : 0.742 9.988 8226 Z= 0.379 Chirality : 0.045 0.262 974 Planarity : 0.006 0.078 1041 Dihedral : 5.686 39.272 826 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.55 % Favored : 86.56 % Rotamer: Outliers : 2.16 % Allowed : 19.41 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.27 (0.31), residues: 781 helix: 1.47 (0.27), residues: 394 sheet: -2.43 (0.70), residues: 31 loop : -3.64 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.011 0.001 PHE A 395 TYR 0.017 0.001 TYR A 689 ARG 0.003 0.000 ARG A 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1562 Ramachandran restraints generated. 781 Oldfield, 0 Emsley, 781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 PHE cc_start: 0.8866 (m-80) cc_final: 0.8471 (m-80) REVERT: A 689 TYR cc_start: 0.9313 (p90) cc_final: 0.8891 (p90) REVERT: A 705 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8516 (ppp) REVERT: A 799 MET cc_start: 0.9007 (ppp) cc_final: 0.8739 (tmm) outliers start: 14 outliers final: 10 residues processed: 58 average time/residue: 0.1486 time to fit residues: 12.3561 Evaluate side-chains 58 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 845 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 946 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 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 186 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.101795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061302 restraints weight = 24681.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.063130 restraints weight = 10929.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064045 restraints weight = 7190.045| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6057 Z= 0.245 Angle : 0.766 10.213 8226 Z= 0.390 Chirality : 0.045 0.260 974 Planarity : 0.006 0.079 1041 Dihedral : 5.703 39.349 826 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.29 % Favored : 86.81 % Rotamer: Outliers : 2.16 % Allowed : 19.57 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.26 (0.31), residues: 781 helix: 1.42 (0.27), residues: 395 sheet: -2.37 (0.81), residues: 23 loop : -3.57 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 558 HIS 0.011 0.001 HIS A 473 PHE 0.011 0.001 PHE A 395 TYR 0.017 0.001 TYR A 689 ARG 0.002 0.000 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1518.35 seconds wall clock time: 27 minutes 59.34 seconds (1679.34 seconds total)