Starting phenix.real_space_refine on Fri Dec 27 15:07:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvv_37873/12_2024/8wvv_37873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvv_37873/12_2024/8wvv_37873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wvv_37873/12_2024/8wvv_37873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvv_37873/12_2024/8wvv_37873.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvv_37873/12_2024/8wvv_37873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvv_37873/12_2024/8wvv_37873.cif" } resolution = 3.35 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= 0.006 sd= 0.044 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 26 5.16 5 C 3643 2.51 5 N 918 2.21 5 O 1009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5596 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5596 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 35, 'TRANS': 682} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.95, per 1000 atoms: 0.71 Number of scatterers: 5596 At special positions: 0 Unit cell: (77.08, 93.48, 136.94, 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 26 16.00 O 1009 8.00 N 918 7.00 C 3643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=1.99 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.07 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: 1.31 Conformation dependent library (CDL) restraints added in 771.9 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 5 sheets defined 33.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.694A pdb=" N ALA A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 466 through 474 removed outlier: 4.158A pdb=" N CYS A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.665A pdb=" N ASN A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.837A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 614 removed outlier: 3.915A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 644 removed outlier: 4.319A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 658 through 675 removed outlier: 3.560A pdb=" N PHE A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 4.214A pdb=" N LEU A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 729 removed outlier: 3.846A pdb=" N LEU A 713 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR A 725 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 729 " --> pdb=" O TYR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 768 removed outlier: 3.564A pdb=" N ASN A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 780 through 789 Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.728A pdb=" N ASN A 797 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 817 removed outlier: 3.715A pdb=" N LEU A 814 " --> pdb=" O GLU A 810 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 5.841A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A 62 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 110 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 134 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 206 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU A 253 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 304 removed outlier: 7.578A pdb=" N LEU A 301 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR A 327 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE A 303 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 169 hydrogen bonds defined for protein. 498 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: 1.82 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 891 1.30 - 1.43: 1491 1.43 - 1.56: 3309 1.56 - 1.69: 1 1.69 - 1.82: 35 Bond restraints: 5727 Sorted by residual: bond pdb=" C ASN A 805 " pdb=" N PRO A 806 " ideal model delta sigma weight residual 1.335 1.507 -0.172 1.19e-02 7.06e+03 2.09e+02 bond pdb=" C TYR A 468 " pdb=" O TYR A 468 " ideal model delta sigma weight residual 1.236 1.341 -0.105 1.26e-02 6.30e+03 6.88e+01 bond pdb=" C PHE A 759 " pdb=" O PHE A 759 " ideal model delta sigma weight residual 1.236 1.308 -0.072 1.15e-02 7.56e+03 3.89e+01 bond pdb=" CA SER A 690 " pdb=" CB SER A 690 " ideal model delta sigma weight residual 1.538 1.459 0.079 1.38e-02 5.25e+03 3.32e+01 bond pdb=" C ILE A 758 " pdb=" O ILE A 758 " ideal model delta sigma weight residual 1.237 1.301 -0.064 1.12e-02 7.97e+03 3.31e+01 ... (remaining 5722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.83: 7691 4.83 - 9.67: 81 9.67 - 14.50: 12 14.50 - 19.33: 3 19.33 - 24.17: 1 Bond angle restraints: 7788 Sorted by residual: angle pdb=" N ALA A 689 " pdb=" CA ALA A 689 " pdb=" C ALA A 689 " ideal model delta sigma weight residual 114.62 90.45 24.17 1.14e+00 7.69e-01 4.49e+02 angle pdb=" C ASN A 805 " pdb=" N PRO A 806 " pdb=" CA PRO A 806 " ideal model delta sigma weight residual 119.56 135.00 -15.44 1.02e+00 9.61e-01 2.29e+02 angle pdb=" C TYR A 801 " pdb=" CA TYR A 801 " pdb=" CB TYR A 801 " ideal model delta sigma weight residual 110.79 92.20 18.59 1.66e+00 3.63e-01 1.25e+02 angle pdb=" N SER A 573 " pdb=" CA SER A 573 " pdb=" C SER A 573 " ideal model delta sigma weight residual 113.18 101.03 12.15 1.21e+00 6.83e-01 1.01e+02 angle pdb=" C LEU A 575 " pdb=" N PHE A 576 " pdb=" CA PHE A 576 " ideal model delta sigma weight residual 120.54 108.55 11.99 1.35e+00 5.49e-01 7.88e+01 ... (remaining 7783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 2845 16.90 - 33.80: 422 33.80 - 50.70: 106 50.70 - 67.59: 20 67.59 - 84.49: 9 Dihedral angle restraints: 3402 sinusoidal: 1318 harmonic: 2084 Sorted by residual: dihedral pdb=" C TYR A 801 " pdb=" N TYR A 801 " pdb=" CA TYR A 801 " pdb=" CB TYR A 801 " ideal model delta harmonic sigma weight residual -122.60 -98.42 -24.18 0 2.50e+00 1.60e-01 9.36e+01 dihedral pdb=" C PHE A 804 " pdb=" N PHE A 804 " pdb=" CA PHE A 804 " pdb=" CB PHE A 804 " ideal model delta harmonic sigma weight residual -122.60 -145.59 22.99 0 2.50e+00 1.60e-01 8.46e+01 dihedral pdb=" C SER A 688 " pdb=" N SER A 688 " pdb=" CA SER A 688 " pdb=" CB SER A 688 " ideal model delta harmonic sigma weight residual -122.60 -101.73 -20.87 0 2.50e+00 1.60e-01 6.97e+01 ... (remaining 3399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 901 0.178 - 0.357: 10 0.357 - 0.535: 7 0.535 - 0.713: 1 0.713 - 0.892: 1 Chirality restraints: 920 Sorted by residual: chirality pdb=" CA PHE A 804 " pdb=" N PHE A 804 " pdb=" C PHE A 804 " pdb=" CB PHE A 804 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA PHE A 803 " pdb=" N PHE A 803 " pdb=" C PHE A 803 " pdb=" CB PHE A 803 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CA SER A 688 " pdb=" N SER A 688 " pdb=" C SER A 688 " pdb=" CB SER A 688 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 6.92e+00 ... (remaining 917 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 562 " -0.033 2.00e-02 2.50e+03 6.69e-02 4.48e+01 pdb=" C THR A 562 " 0.116 2.00e-02 2.50e+03 pdb=" O THR A 562 " -0.044 2.00e-02 2.50e+03 pdb=" N THR A 563 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 679 " -0.099 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO A 680 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO A 680 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 680 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 570 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO A 571 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " 0.063 5.00e-02 4.00e+02 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 15 2.33 - 2.98: 3001 2.98 - 3.62: 8782 3.62 - 4.26: 13457 4.26 - 4.90: 21703 Nonbonded interactions: 46958 Sorted by model distance: nonbonded pdb=" O GLY A 592 " pdb=" CD2 PHE A 596 " model vdw 1.693 3.340 nonbonded pdb=" CD2 PHE A 555 " pdb=" CG2 VAL A 799 " model vdw 1.729 3.760 nonbonded pdb=" CE2 PHE A 555 " pdb=" CG2 VAL A 799 " model vdw 2.171 3.760 nonbonded pdb=" O VAL A 153 " pdb=" OG1 THR A 178 " model vdw 2.174 3.040 nonbonded pdb=" O VAL A 711 " pdb=" OG SER A 715 " model vdw 2.179 3.040 ... (remaining 46953 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.140 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: 0.010 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: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.007 0.172 5727 Z= 0.443 Angle : 1.257 24.165 7788 Z= 0.813 Chirality : 0.077 0.892 920 Planarity : 0.010 0.142 981 Dihedral : 17.092 84.492 2025 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.28 % Allowed : 25.68 % Favored : 73.05 % Cbeta Deviations : 1.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -2.78 (0.30), residues: 704 helix: -1.61 (0.32), residues: 228 sheet: -3.17 (0.60), residues: 72 loop : -1.71 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 812 HIS 0.003 0.001 HIS A 171 PHE 0.045 0.002 PHE A 808 TYR 0.028 0.002 TYR A 801 ARG 0.003 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 HIS cc_start: 0.7810 (t70) cc_final: 0.7363 (t70) REVERT: A 371 SER cc_start: 0.8914 (p) cc_final: 0.8545 (p) REVERT: A 762 PRO cc_start: 0.8048 (Cg_exo) cc_final: 0.7806 (Cg_endo) outliers start: 8 outliers final: 7 residues processed: 117 average time/residue: 0.1485 time to fit residues: 23.6964 Evaluate side-chains 109 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 571 PRO Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 783 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 HIS A 417 ASN A 458 ASN A 584 ASN A 748 HIS A 797 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5727 Z= 0.252 Angle : 0.683 8.303 7788 Z= 0.343 Chirality : 0.045 0.161 920 Planarity : 0.006 0.077 981 Dihedral : 5.960 57.798 757 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.15 % Allowed : 24.40 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -2.38 (0.30), residues: 704 helix: -0.93 (0.32), residues: 224 sheet: -3.14 (0.56), residues: 72 loop : -1.66 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.006 0.001 HIS A 748 PHE 0.035 0.002 PHE A 596 TYR 0.020 0.002 TYR A 280 ARG 0.003 0.000 ARG A 817 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.7830 (t80) cc_final: 0.7360 (t80) REVERT: A 245 LYS cc_start: 0.8547 (tttt) cc_final: 0.8335 (tppt) REVERT: A 273 LEU cc_start: 0.8696 (mm) cc_final: 0.8168 (tp) REVERT: A 371 SER cc_start: 0.8910 (p) cc_final: 0.8478 (p) REVERT: A 395 ASP cc_start: 0.7422 (t70) cc_final: 0.7060 (t0) REVERT: A 442 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 520 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7667 (mp) REVERT: A 671 LEU cc_start: 0.8216 (tp) cc_final: 0.7981 (mt) REVERT: A 728 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7428 (mm) REVERT: A 731 ASN cc_start: 0.7623 (p0) cc_final: 0.7277 (t0) REVERT: A 783 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7357 (tptp) REVERT: A 808 PHE cc_start: 0.7991 (t80) cc_final: 0.7732 (t80) outliers start: 26 outliers final: 14 residues processed: 133 average time/residue: 0.1195 time to fit residues: 23.0452 Evaluate side-chains 126 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5727 Z= 0.245 Angle : 0.663 8.989 7788 Z= 0.328 Chirality : 0.045 0.183 920 Planarity : 0.005 0.065 981 Dihedral : 5.353 50.626 748 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.94 % Allowed : 23.76 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.30), residues: 704 helix: -0.56 (0.33), residues: 225 sheet: -3.19 (0.56), residues: 72 loop : -1.62 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 751 HIS 0.003 0.001 HIS A 209 PHE 0.019 0.001 PHE A 808 TYR 0.019 0.002 TYR A 280 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.8756 (mm) cc_final: 0.8221 (tp) REVERT: A 371 SER cc_start: 0.9001 (p) cc_final: 0.8595 (p) REVERT: A 395 ASP cc_start: 0.7487 (t70) cc_final: 0.7120 (t0) REVERT: A 520 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7818 (mp) REVERT: A 671 LEU cc_start: 0.8206 (tp) cc_final: 0.7969 (mt) REVERT: A 725 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7101 (t80) REVERT: A 728 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7497 (mm) REVERT: A 731 ASN cc_start: 0.7706 (p0) cc_final: 0.7220 (t0) REVERT: A 783 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7383 (tptp) outliers start: 31 outliers final: 12 residues processed: 130 average time/residue: 0.1345 time to fit residues: 25.5639 Evaluate side-chains 118 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 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: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5727 Z= 0.217 Angle : 0.636 7.717 7788 Z= 0.314 Chirality : 0.044 0.159 920 Planarity : 0.005 0.067 981 Dihedral : 5.109 46.118 748 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.63 % Allowed : 24.56 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -2.03 (0.30), residues: 704 helix: -0.30 (0.33), residues: 226 sheet: -3.18 (0.56), residues: 72 loop : -1.62 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.004 0.001 HIS A 97 PHE 0.019 0.001 PHE A 808 TYR 0.016 0.002 TYR A 801 ARG 0.003 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.650 Fit side-chains REVERT: A 273 LEU cc_start: 0.8708 (mm) cc_final: 0.8215 (tp) REVERT: A 371 SER cc_start: 0.8952 (p) cc_final: 0.8551 (p) REVERT: A 395 ASP cc_start: 0.7523 (t70) cc_final: 0.7162 (t0) REVERT: A 473 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6922 (t80) REVERT: A 595 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8383 (m) REVERT: A 671 LEU cc_start: 0.8195 (tp) cc_final: 0.7962 (mt) REVERT: A 728 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7422 (mm) REVERT: A 783 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7506 (tptp) outliers start: 29 outliers final: 13 residues processed: 127 average time/residue: 0.1288 time to fit residues: 23.5105 Evaluate side-chains 120 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5727 Z= 0.294 Angle : 0.663 8.414 7788 Z= 0.330 Chirality : 0.046 0.161 920 Planarity : 0.005 0.068 981 Dihedral : 5.366 46.013 748 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.78 % Allowed : 24.88 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.30), residues: 704 helix: -0.40 (0.33), residues: 225 sheet: -3.22 (0.56), residues: 72 loop : -1.60 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 474 HIS 0.003 0.001 HIS A 521 PHE 0.024 0.002 PHE A 808 TYR 0.018 0.002 TYR A 801 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.655 Fit side-chains REVERT: A 273 LEU cc_start: 0.8729 (mm) cc_final: 0.8232 (tp) REVERT: A 371 SER cc_start: 0.8985 (p) cc_final: 0.8575 (p) REVERT: A 395 ASP cc_start: 0.7508 (t70) cc_final: 0.7150 (t0) REVERT: A 416 THR cc_start: 0.8628 (m) cc_final: 0.8405 (t) REVERT: A 473 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6932 (t80) REVERT: A 671 LEU cc_start: 0.8220 (tp) cc_final: 0.7965 (mt) REVERT: A 728 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7473 (mm) REVERT: A 731 ASN cc_start: 0.7491 (p0) cc_final: 0.7177 (p0) REVERT: A 783 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7508 (tptp) outliers start: 30 outliers final: 20 residues processed: 124 average time/residue: 0.1177 time to fit residues: 21.2090 Evaluate side-chains 118 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5727 Z= 0.285 Angle : 0.644 7.525 7788 Z= 0.322 Chirality : 0.045 0.155 920 Planarity : 0.005 0.069 981 Dihedral : 5.309 45.647 748 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.78 % Allowed : 26.48 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.31), residues: 704 helix: -0.27 (0.34), residues: 226 sheet: -3.28 (0.55), residues: 72 loop : -1.59 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.004 0.001 HIS A 157 PHE 0.020 0.001 PHE A 808 TYR 0.015 0.002 TYR A 801 ARG 0.003 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.631 Fit side-chains REVERT: A 273 LEU cc_start: 0.8758 (mm) cc_final: 0.8256 (tp) REVERT: A 371 SER cc_start: 0.8995 (p) cc_final: 0.8577 (p) REVERT: A 395 ASP cc_start: 0.7519 (t70) cc_final: 0.7156 (t0) REVERT: A 416 THR cc_start: 0.8645 (m) cc_final: 0.8428 (t) REVERT: A 473 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.7005 (t80) REVERT: A 542 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7391 (ttm110) REVERT: A 671 LEU cc_start: 0.8211 (tp) cc_final: 0.7948 (mt) REVERT: A 728 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7465 (mm) REVERT: A 731 ASN cc_start: 0.7467 (p0) cc_final: 0.7189 (p0) REVERT: A 783 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7518 (tptp) outliers start: 30 outliers final: 20 residues processed: 123 average time/residue: 0.1291 time to fit residues: 22.5530 Evaluate side-chains 118 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.0070 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5727 Z= 0.182 Angle : 0.604 8.435 7788 Z= 0.298 Chirality : 0.043 0.139 920 Planarity : 0.005 0.070 981 Dihedral : 4.839 42.181 748 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.51 % Allowed : 27.43 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.73 (0.31), residues: 704 helix: -0.00 (0.35), residues: 226 sheet: -2.74 (0.69), residues: 52 loop : -1.63 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 474 HIS 0.002 0.001 HIS A 97 PHE 0.024 0.001 PHE A 95 TYR 0.015 0.001 TYR A 801 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8117 (tp) REVERT: A 273 LEU cc_start: 0.8734 (mm) cc_final: 0.8228 (tp) REVERT: A 371 SER cc_start: 0.8948 (p) cc_final: 0.8531 (p) REVERT: A 416 THR cc_start: 0.8599 (m) cc_final: 0.8338 (t) REVERT: A 473 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7101 (t80) REVERT: A 562 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7440 (p) REVERT: A 671 LEU cc_start: 0.8160 (tp) cc_final: 0.7878 (mt) REVERT: A 728 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7359 (mm) outliers start: 22 outliers final: 15 residues processed: 117 average time/residue: 0.1339 time to fit residues: 22.5119 Evaluate side-chains 119 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 802 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5727 Z= 0.215 Angle : 0.640 10.860 7788 Z= 0.314 Chirality : 0.044 0.145 920 Planarity : 0.005 0.069 981 Dihedral : 4.377 30.054 742 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.83 % Allowed : 27.11 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.76 (0.31), residues: 704 helix: 0.04 (0.35), residues: 225 sheet: -3.02 (0.63), residues: 61 loop : -1.60 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.004 0.001 HIS A 209 PHE 0.036 0.001 PHE A 808 TYR 0.014 0.002 TYR A 801 ARG 0.002 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.574 Fit side-chains REVERT: A 182 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 273 LEU cc_start: 0.8738 (mm) cc_final: 0.8225 (tp) REVERT: A 371 SER cc_start: 0.8971 (p) cc_final: 0.8492 (p) REVERT: A 395 ASP cc_start: 0.7614 (t0) cc_final: 0.7135 (t0) REVERT: A 473 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.7086 (t80) REVERT: A 562 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7306 (p) REVERT: A 671 LEU cc_start: 0.8164 (tp) cc_final: 0.7892 (mt) REVERT: A 728 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7360 (mm) outliers start: 24 outliers final: 16 residues processed: 119 average time/residue: 0.1222 time to fit residues: 21.1920 Evaluate side-chains 118 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 0.0670 chunk 60 optimal weight: 0.0060 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5727 Z= 0.189 Angle : 0.652 12.782 7788 Z= 0.314 Chirality : 0.044 0.140 920 Planarity : 0.005 0.069 981 Dihedral : 4.280 28.967 742 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.51 % Allowed : 28.23 % Favored : 68.26 % 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: -1.68 (0.31), residues: 704 helix: 0.06 (0.35), residues: 224 sheet: -2.94 (0.65), residues: 61 loop : -1.51 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.027 0.001 PHE A 808 TYR 0.013 0.001 TYR A 801 ARG 0.002 0.000 ARG A 643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.665 Fit side-chains REVERT: A 182 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8110 (tp) REVERT: A 273 LEU cc_start: 0.8700 (mm) cc_final: 0.8154 (tp) REVERT: A 371 SER cc_start: 0.8801 (p) cc_final: 0.8361 (p) REVERT: A 395 ASP cc_start: 0.7596 (t0) cc_final: 0.7096 (t0) REVERT: A 473 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.7122 (t80) REVERT: A 671 LEU cc_start: 0.8169 (tp) cc_final: 0.7913 (mt) REVERT: A 728 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7347 (mm) REVERT: A 743 SER cc_start: 0.8693 (p) cc_final: 0.8238 (t) outliers start: 22 outliers final: 14 residues processed: 112 average time/residue: 0.1238 time to fit residues: 20.4161 Evaluate side-chains 110 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.0040 chunk 60 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5727 Z= 0.184 Angle : 0.654 12.663 7788 Z= 0.315 Chirality : 0.044 0.173 920 Planarity : 0.005 0.077 981 Dihedral : 4.304 32.856 742 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.87 % Allowed : 29.03 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.56 (0.31), residues: 704 helix: 0.21 (0.35), residues: 223 sheet: -2.62 (0.74), residues: 47 loop : -1.58 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.027 0.001 PHE A 808 TYR 0.011 0.002 TYR A 234 ARG 0.005 0.000 ARG A 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.816 Fit side-chains REVERT: A 182 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8113 (tp) REVERT: A 273 LEU cc_start: 0.8682 (mm) cc_final: 0.8127 (tp) REVERT: A 395 ASP cc_start: 0.7611 (t0) cc_final: 0.7158 (t0) REVERT: A 671 LEU cc_start: 0.8140 (tp) cc_final: 0.7845 (mt) REVERT: A 728 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7334 (mm) REVERT: A 743 SER cc_start: 0.8862 (p) cc_final: 0.8354 (t) outliers start: 18 outliers final: 14 residues processed: 110 average time/residue: 0.1254 time to fit residues: 20.0037 Evaluate side-chains 112 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 0.0000 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** 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 = 0.4009 r_free = 0.4009 target = 0.124313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102307 restraints weight = 12410.920| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.68 r_work: 0.3536 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5727 Z= 0.185 Angle : 0.657 12.187 7788 Z= 0.315 Chirality : 0.044 0.146 920 Planarity : 0.005 0.071 981 Dihedral : 4.310 33.734 742 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.19 % Allowed : 28.71 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.55 (0.31), residues: 704 helix: 0.24 (0.35), residues: 223 sheet: -2.66 (0.73), residues: 47 loop : -1.59 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.003 0.001 HIS A 209 PHE 0.027 0.001 PHE A 95 TYR 0.011 0.001 TYR A 234 ARG 0.004 0.000 ARG A 604 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1580.38 seconds wall clock time: 29 minutes 33.17 seconds (1773.17 seconds total)