Starting phenix.real_space_refine on Thu Jul 2 05:01:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sva_25446/07_2026/7sva_25446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sva_25446/07_2026/7sva_25446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sva_25446/07_2026/7sva_25446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sva_25446/07_2026/7sva_25446.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sva_25446/07_2026/7sva_25446.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sva_25446/07_2026/7sva_25446.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sva_25446/07_2026/7sva_25446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sva_25446/07_2026/7sva_25446.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 93 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 4090 2.51 5 N 1159 2.21 5 O 1217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6515 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6290 Classifications: {'peptide': 792} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 747} Chain breaks: 5 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 224 Classifications: {'DNA': 1, 'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 6} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6515 At special positions: 0 Unit cell: (77.542, 95.088, 113.766, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 11 15.00 Mg 1 11.99 O 1217 8.00 N 1159 7.00 C 4090 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 535.2 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 31.4% alpha, 17.7% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.690A pdb=" N LEU A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 283 removed outlier: 5.121A pdb=" N LEU A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 460 through 472 removed outlier: 4.205A pdb=" N THR A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.731A pdb=" N ALA A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 565 through 584 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 658 through 663 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.671A pdb=" N VAL A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 770 through 784 removed outlier: 3.703A pdb=" N ASP A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 821 removed outlier: 3.955A pdb=" N ILE A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 821 " --> pdb=" O CYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 915 removed outlier: 3.541A pdb=" N CYS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing sheet with id=AA1, first strand: chain 'A' and resid 738 through 745 removed outlier: 3.751A pdb=" N ALA A 724 " --> pdb=" O CYS A 743 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE A 705 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 710 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 790 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE A 831 " --> pdb=" O ILE A 790 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE A 792 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A 833 " --> pdb=" O PHE A 792 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG A 794 " --> pdb=" O VAL A 833 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 315 through 318 removed outlier: 3.794A pdb=" N LEU A 322 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 503 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 197 removed outlier: 7.179A pdb=" N GLN A 159 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 241 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 214 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291 removed outlier: 4.031A pdb=" N PHE A 311 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 387 removed outlier: 3.600A pdb=" N VAL A 373 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 371 " --> pdb=" O VAL A 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 394 removed outlier: 4.665A pdb=" N GLY A 389 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 432 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 391 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N CYS A 430 " --> pdb=" O THR A 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.542A pdb=" N VAL A 686 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 596 through 597 removed outlier: 4.187A pdb=" N TYR A 596 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 556 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE A 629 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 558 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N CYS A 656 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 628 " --> pdb=" O CYS A 656 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.80 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: 2082 1.34 - 1.46: 1074 1.46 - 1.58: 3446 1.58 - 1.70: 21 1.70 - 1.81: 52 Bond restraints: 6675 Sorted by residual: bond pdb=" N SER A 720 " pdb=" CA SER A 720 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.29e-02 6.01e+03 6.04e+00 bond pdb=" N GLU A 718 " pdb=" CA GLU A 718 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 4.96e+00 bond pdb=" N ARG A 780 " pdb=" CA ARG A 780 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.96e+00 bond pdb=" N SER A 719 " pdb=" CA SER A 719 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.95e+00 bond pdb=" N ASN A 715 " pdb=" CA ASN A 715 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.27e+00 ... (remaining 6670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 8950 2.22 - 4.43: 119 4.43 - 6.65: 10 6.65 - 8.86: 3 8.86 - 11.08: 2 Bond angle restraints: 9084 Sorted by residual: angle pdb=" N TRP A 732 " pdb=" CA TRP A 732 " pdb=" C TRP A 732 " ideal model delta sigma weight residual 109.81 119.53 -9.72 2.21e+00 2.05e-01 1.93e+01 angle pdb=" C LYS A 457 " pdb=" CA LYS A 457 " pdb=" CB LYS A 457 " ideal model delta sigma weight residual 116.34 110.51 5.83 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA LEU A 368 " pdb=" CB LEU A 368 " pdb=" CG LEU A 368 " ideal model delta sigma weight residual 116.30 127.38 -11.08 3.50e+00 8.16e-02 1.00e+01 angle pdb=" CA GLU A 718 " pdb=" C GLU A 718 " pdb=" O GLU A 718 " ideal model delta sigma weight residual 120.90 117.91 2.99 1.07e+00 8.73e-01 7.81e+00 angle pdb=" CA GLU A 717 " pdb=" C GLU A 717 " pdb=" O GLU A 717 " ideal model delta sigma weight residual 122.32 118.31 4.01 1.51e+00 4.39e-01 7.07e+00 ... (remaining 9079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 3527 16.86 - 33.72: 406 33.72 - 50.58: 78 50.58 - 67.44: 18 67.44 - 84.30: 10 Dihedral angle restraints: 4039 sinusoidal: 1729 harmonic: 2310 Sorted by residual: dihedral pdb=" CA GLY A 856 " pdb=" C GLY A 856 " pdb=" N ASN A 857 " pdb=" CA ASN A 857 " ideal model delta harmonic sigma weight residual 180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TRP A 732 " pdb=" C TRP A 732 " pdb=" N PRO A 733 " pdb=" CA PRO A 733 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASN A 548 " pdb=" C ASN A 548 " pdb=" N GLY A 549 " pdb=" CA GLY A 549 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 859 0.056 - 0.112: 143 0.112 - 0.167: 14 0.167 - 0.223: 0 0.223 - 0.279: 1 Chirality restraints: 1017 Sorted by residual: chirality pdb=" CA TRP A 732 " pdb=" N TRP A 732 " pdb=" C TRP A 732 " pdb=" CB TRP A 732 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CB ILE A 701 " pdb=" CA ILE A 701 " pdb=" CG1 ILE A 701 " pdb=" CG2 ILE A 701 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1014 not shown) Planarity restraints: 1131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.032 2.00e-02 2.50e+03 2.88e-02 2.07e+01 pdb=" CG TRP A 732 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 695 " -0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A 696 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 696 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 696 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 732 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO A 733 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 733 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 733 " -0.031 5.00e-02 4.00e+02 ... (remaining 1128 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 76 2.64 - 3.21: 5713 3.21 - 3.77: 10012 3.77 - 4.34: 13415 4.34 - 4.90: 22923 Nonbonded interactions: 52139 Sorted by model distance: nonbonded pdb=" OD2 ASP A 709 " pdb="MG MG A1001 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP A 709 " pdb="MG MG A1001 " model vdw 2.097 2.170 nonbonded pdb=" O ARG A 643 " pdb=" OG1 THR A 647 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR A 829 " pdb=" OD1 ASN A 900 " model vdw 2.177 3.040 nonbonded pdb=" OE1 GLU A 646 " pdb=" OH TYR A 944 " model vdw 2.192 3.040 ... (remaining 52134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.030 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6675 Z= 0.141 Angle : 0.595 11.079 9084 Z= 0.316 Chirality : 0.042 0.279 1017 Planarity : 0.005 0.089 1131 Dihedral : 14.904 84.303 2545 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.32), residues: 780 helix: 1.87 (0.35), residues: 239 sheet: -1.04 (0.40), residues: 179 loop : -1.39 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 300 TYR 0.007 0.001 TYR A 312 PHE 0.011 0.001 PHE A 802 TRP 0.077 0.003 TRP A 732 HIS 0.001 0.000 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 6675) covalent geometry : angle 0.59544 / 0.32 ( 9084) hydrogen bonds : bond 0.16783 / 10.62 ( 245) hydrogen bonds : angle 6.79600 / 4.99 ( 708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.1447 time to fit residues: 9.8527 Evaluate side-chains 26 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 427 HIS A 489 ASN A 677 ASN A 715 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.054348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.040526 restraints weight = 34728.629| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.41 r_work: 0.2818 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6675 Z= 0.183 Angle : 0.617 10.136 9084 Z= 0.311 Chirality : 0.043 0.162 1017 Planarity : 0.005 0.059 1131 Dihedral : 7.268 64.366 991 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.43 % Allowed : 6.37 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.32), residues: 780 helix: 1.99 (0.36), residues: 242 sheet: -0.86 (0.40), residues: 177 loop : -1.32 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 474 TYR 0.011 0.001 TYR A 596 PHE 0.013 0.001 PHE A 211 TRP 0.026 0.002 TRP A 732 HIS 0.004 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 6675) covalent geometry : angle 0.61659 / 0.31 ( 9084) hydrogen bonds : bond 0.03551 / 2.46 ( 245) hydrogen bonds : angle 4.93500 / 3.56 ( 708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.9296 (t0) cc_final: 0.8940 (p0) REVERT: A 848 ASP cc_start: 0.8894 (t0) cc_final: 0.8607 (t0) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.1260 time to fit residues: 5.2745 Evaluate side-chains 28 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.053825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040201 restraints weight = 34818.509| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.32 r_work: 0.2799 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6675 Z= 0.192 Angle : 0.584 7.425 9084 Z= 0.298 Chirality : 0.042 0.149 1017 Planarity : 0.005 0.052 1131 Dihedral : 7.175 55.924 991 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.72 % Allowed : 8.83 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.32), residues: 780 helix: 2.07 (0.35), residues: 243 sheet: -0.91 (0.40), residues: 172 loop : -1.37 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 789 TYR 0.010 0.001 TYR A 596 PHE 0.010 0.001 PHE A 211 TRP 0.013 0.002 TRP A 732 HIS 0.003 0.001 HIS A 894 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 6675) covalent geometry : angle 0.58401 / 0.30 ( 9084) hydrogen bonds : bond 0.03405 / 2.36 ( 245) hydrogen bonds : angle 4.69899 / 3.37 ( 708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.9281 (t0) cc_final: 0.8927 (p0) REVERT: A 630 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 848 ASP cc_start: 0.8921 (t0) cc_final: 0.8631 (t0) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.0979 time to fit residues: 4.9800 Evaluate side-chains 33 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 823 ASN A 838 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.053022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.039453 restraints weight = 35468.770| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.37 r_work: 0.2767 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6675 Z= 0.267 Angle : 0.644 6.548 9084 Z= 0.330 Chirality : 0.044 0.148 1017 Planarity : 0.006 0.058 1131 Dihedral : 7.537 61.396 991 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.59 % Allowed : 10.85 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.31), residues: 780 helix: 1.77 (0.34), residues: 240 sheet: -1.02 (0.40), residues: 168 loop : -1.43 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 789 TYR 0.012 0.002 TYR A 596 PHE 0.011 0.002 PHE A 874 TRP 0.012 0.002 TRP A 732 HIS 0.004 0.001 HIS A 894 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.27 ( 6675) covalent geometry : angle 0.64446 / 0.33 ( 9084) hydrogen bonds : bond 0.03632 / 2.57 ( 245) hydrogen bonds : angle 4.77212 / 3.40 ( 708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.9259 (t0) cc_final: 0.8940 (p0) REVERT: A 550 MET cc_start: 0.8751 (mmp) cc_final: 0.8418 (mmm) REVERT: A 630 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8707 (pp) outliers start: 11 outliers final: 5 residues processed: 38 average time/residue: 0.0683 time to fit residues: 3.9011 Evaluate side-chains 32 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.053454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.039863 restraints weight = 35725.896| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.31 r_work: 0.2783 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6675 Z= 0.188 Angle : 0.578 6.538 9084 Z= 0.297 Chirality : 0.042 0.150 1017 Planarity : 0.005 0.046 1131 Dihedral : 7.339 58.078 991 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.45 % Allowed : 12.74 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.31), residues: 780 helix: 1.96 (0.34), residues: 241 sheet: -1.01 (0.40), residues: 168 loop : -1.42 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 789 TYR 0.013 0.001 TYR A 893 PHE 0.010 0.001 PHE A 291 TRP 0.007 0.001 TRP A 732 HIS 0.004 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 6675) covalent geometry : angle 0.57760 / 0.30 ( 9084) hydrogen bonds : bond 0.03277 / 2.30 ( 245) hydrogen bonds : angle 4.60327 / 3.28 ( 708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.9273 (t0) cc_final: 0.8959 (p0) REVERT: A 550 MET cc_start: 0.8730 (mmp) cc_final: 0.8380 (mmm) REVERT: A 630 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8694 (pp) REVERT: A 848 ASP cc_start: 0.8932 (t0) cc_final: 0.8652 (t0) outliers start: 10 outliers final: 6 residues processed: 38 average time/residue: 0.0774 time to fit residues: 4.1182 Evaluate side-chains 33 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.053012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.039477 restraints weight = 36555.238| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 4.44 r_work: 0.2759 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 6675 Z= 0.306 Angle : 0.674 7.135 9084 Z= 0.345 Chirality : 0.044 0.150 1017 Planarity : 0.006 0.050 1131 Dihedral : 7.803 65.890 991 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.74 % Allowed : 13.46 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.30), residues: 780 helix: 1.65 (0.34), residues: 241 sheet: -1.03 (0.39), residues: 172 loop : -1.57 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 789 TYR 0.015 0.002 TYR A 596 PHE 0.011 0.002 PHE A 255 TRP 0.011 0.002 TRP A 732 HIS 0.006 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.31 ( 6675) covalent geometry : angle 0.67374 / 0.34 ( 9084) hydrogen bonds : bond 0.03797 / 2.70 ( 245) hydrogen bonds : angle 4.80671 / 3.40 ( 708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.9280 (t0) cc_final: 0.8980 (p0) REVERT: A 550 MET cc_start: 0.8818 (mmp) cc_final: 0.8595 (mmm) REVERT: A 630 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8688 (pp) REVERT: A 852 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8069 (p) outliers start: 12 outliers final: 8 residues processed: 38 average time/residue: 0.0708 time to fit residues: 3.8304 Evaluate side-chains 37 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.053700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.040224 restraints weight = 35242.360| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 4.36 r_work: 0.2807 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6675 Z= 0.139 Angle : 0.546 6.479 9084 Z= 0.280 Chirality : 0.041 0.149 1017 Planarity : 0.004 0.044 1131 Dihedral : 7.310 58.047 991 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.03 % Allowed : 13.89 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.31), residues: 780 helix: 2.01 (0.34), residues: 241 sheet: -0.90 (0.39), residues: 176 loop : -1.48 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 789 TYR 0.012 0.001 TYR A 596 PHE 0.010 0.001 PHE A 148 TRP 0.006 0.001 TRP A 732 HIS 0.004 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 6675) covalent geometry : angle 0.54625 / 0.28 ( 9084) hydrogen bonds : bond 0.03054 / 2.13 ( 245) hydrogen bonds : angle 4.48590 / 3.19 ( 708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.9293 (t0) cc_final: 0.8990 (p0) REVERT: A 254 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8143 (mt-10) REVERT: A 630 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8661 (pp) REVERT: A 771 MET cc_start: 0.8445 (mtt) cc_final: 0.8200 (mtt) outliers start: 14 outliers final: 7 residues processed: 43 average time/residue: 0.0857 time to fit residues: 5.0190 Evaluate side-chains 36 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 854 ARG Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.053676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.040212 restraints weight = 35720.408| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.39 r_work: 0.2801 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6675 Z= 0.153 Angle : 0.575 6.813 9084 Z= 0.293 Chirality : 0.042 0.198 1017 Planarity : 0.004 0.042 1131 Dihedral : 7.227 55.338 991 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.45 % Allowed : 14.62 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.31), residues: 780 helix: 2.02 (0.34), residues: 240 sheet: -0.67 (0.40), residues: 166 loop : -1.48 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 562 TYR 0.011 0.001 TYR A 596 PHE 0.009 0.001 PHE A 211 TRP 0.008 0.001 TRP A 732 HIS 0.004 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 6675) covalent geometry : angle 0.57489 / 0.29 ( 9084) hydrogen bonds : bond 0.03079 / 2.17 ( 245) hydrogen bonds : angle 4.46121 / 3.16 ( 708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.9280 (t0) cc_final: 0.8978 (p0) REVERT: A 259 LYS cc_start: 0.8434 (mtmm) cc_final: 0.8207 (pttm) REVERT: A 550 MET cc_start: 0.8782 (mmp) cc_final: 0.8421 (mmm) REVERT: A 630 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 771 MET cc_start: 0.8451 (mtt) cc_final: 0.8230 (mtt) outliers start: 10 outliers final: 9 residues processed: 41 average time/residue: 0.0988 time to fit residues: 5.4200 Evaluate side-chains 38 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 854 ARG Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.053687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040241 restraints weight = 35852.407| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.38 r_work: 0.2803 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6675 Z= 0.152 Angle : 0.577 7.916 9084 Z= 0.292 Chirality : 0.042 0.194 1017 Planarity : 0.004 0.042 1131 Dihedral : 7.120 55.307 990 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.59 % Allowed : 14.47 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.31), residues: 780 helix: 2.00 (0.34), residues: 241 sheet: -0.65 (0.40), residues: 170 loop : -1.47 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 562 TYR 0.012 0.001 TYR A 596 PHE 0.008 0.001 PHE A 211 TRP 0.005 0.001 TRP A 732 HIS 0.004 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6675) covalent geometry : angle 0.57722 / 0.29 ( 9084) hydrogen bonds : bond 0.03025 / 2.13 ( 245) hydrogen bonds : angle 4.42538 / 3.13 ( 708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.9271 (t0) cc_final: 0.8975 (p0) REVERT: A 254 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8353 (mm-30) REVERT: A 291 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8348 (p90) REVERT: A 630 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8571 (pp) REVERT: A 771 MET cc_start: 0.8448 (mtt) cc_final: 0.8239 (mtt) outliers start: 11 outliers final: 8 residues processed: 41 average time/residue: 0.0899 time to fit residues: 5.0778 Evaluate side-chains 39 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 854 ARG Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.052763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.039474 restraints weight = 35787.756| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.36 r_work: 0.2760 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 6675 Z= 0.298 Angle : 0.686 7.218 9084 Z= 0.349 Chirality : 0.045 0.187 1017 Planarity : 0.005 0.048 1131 Dihedral : 7.155 56.917 987 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.88 % Allowed : 13.89 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.30), residues: 780 helix: 1.71 (0.34), residues: 240 sheet: -0.90 (0.40), residues: 164 loop : -1.52 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 562 TYR 0.019 0.002 TYR A 596 PHE 0.011 0.002 PHE A 779 TRP 0.011 0.002 TRP A 732 HIS 0.005 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.30 ( 6675) covalent geometry : angle 0.68572 / 0.35 ( 9084) hydrogen bonds : bond 0.03619 / 2.56 ( 245) hydrogen bonds : angle 4.71666 / 3.33 ( 708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.9270 (t0) cc_final: 0.8989 (p0) REVERT: A 291 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8539 (p90) REVERT: A 630 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8629 (pp) outliers start: 13 outliers final: 10 residues processed: 38 average time/residue: 0.0776 time to fit residues: 4.1602 Evaluate side-chains 39 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 596 TYR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 854 ARG Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.053701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040291 restraints weight = 35257.340| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.35 r_work: 0.2803 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6675 Z= 0.138 Angle : 0.573 8.093 9084 Z= 0.290 Chirality : 0.042 0.174 1017 Planarity : 0.004 0.044 1131 Dihedral : 6.850 55.943 987 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.45 % Allowed : 14.18 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.31), residues: 780 helix: 1.96 (0.34), residues: 240 sheet: -0.60 (0.40), residues: 165 loop : -1.58 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 562 TYR 0.011 0.001 TYR A 596 PHE 0.010 0.001 PHE A 148 TRP 0.005 0.001 TRP A 732 HIS 0.004 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6675) covalent geometry : angle 0.57291 / 0.29 ( 9084) hydrogen bonds : bond 0.03069 / 2.16 ( 245) hydrogen bonds : angle 4.45013 / 3.15 ( 708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.17 seconds wall clock time: 27 minutes 54.64 seconds (1674.64 seconds total)