Starting phenix.real_space_refine on Tue Aug 4 18:15:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vcb_64951/08_2026/9vcb_64951.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vcb_64951/08_2026/9vcb_64951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vcb_64951/08_2026/9vcb_64951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vcb_64951/08_2026/9vcb_64951.map" model { file = "/net/cci-nas-00/data/ceres_data/9vcb_64951/08_2026/9vcb_64951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vcb_64951/08_2026/9vcb_64951.cif" } resolution = 2.82 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= 0.004 sd= 0.133 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 7 5.49 5 S 23 5.16 5 C 3689 2.51 5 N 963 2.21 5 O 982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5665 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5520 Classifications: {'peptide': 705} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 667} Chain breaks: 2 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.15, per 1000 atoms: 0.20 Number of scatterers: 5665 At special positions: 0 Unit cell: (94.0695, 81.8958, 100.71, 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) Zn 1 29.99 S 23 16.00 P 7 15.00 O 982 8.00 N 963 7.00 C 3689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 636 " distance=2.11 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: 0.36 Conformation dependent library (CDL) restraints added in 328.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 682 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 580 " 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 56.5% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 171 through 185 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.996A pdb=" N VAL A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 247 Processing helix chain 'A' and resid 252 through 273 Processing helix chain 'A' and resid 276 through 295 Processing helix chain 'A' and resid 300 through 316 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.632A pdb=" N TRP A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 385 Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.622A pdb=" N LEU A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Proline residue: A 400 - end of helix Processing helix chain 'A' and resid 405 through 424 Processing helix chain 'A' and resid 428 through 451 Proline residue: A 440 - end of helix removed outlier: 4.317A pdb=" N GLY A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 555 through 564 Processing helix chain 'A' and resid 577 through 582 Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 654 through 668 removed outlier: 3.972A pdb=" N MET A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 689 through 697 Processing helix chain 'A' and resid 715 through 724 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 759 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 84 removed outlier: 5.896A pdb=" N ILE A 79 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA A 95 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER A 91 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS A 108 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLY A 158 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG A 110 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL A 160 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR A 112 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS A 162 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N LYS A 114 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 12.440A pdb=" N GLU A 164 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY A 158 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS A 132 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 160 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 130 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 124 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 595 through 598 removed outlier: 9.443A pdb=" N GLN A 595 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP A 569 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 597 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 571 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY A 536 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N PHE A 572 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 538 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 612 through 615 removed outlier: 6.590A pdb=" N VAL A 637 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG A 646 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 678 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 648 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 677 " --> pdb=" O LEU A 702 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 918 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: 0.91 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1000 1.32 - 1.46: 2067 1.46 - 1.59: 2704 1.59 - 1.72: 12 1.72 - 1.86: 39 Bond restraints: 5822 Sorted by residual: bond pdb=" C VAL A 701 " pdb=" O VAL A 701 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.04e-02 9.25e+03 1.80e+01 bond pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta sigma weight residual 1.528 1.467 0.062 1.56e-02 4.11e+03 1.58e+01 bond pdb=" C VAL A 75 " pdb=" O VAL A 75 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.07e-02 8.73e+03 1.37e+01 bond pdb=" CA SER A 62 " pdb=" CB SER A 62 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.63e-02 3.76e+03 1.36e+01 bond pdb=" CA SER A 9 " pdb=" CB SER A 9 " ideal model delta sigma weight residual 1.528 1.470 0.059 1.66e-02 3.63e+03 1.26e+01 ... (remaining 5817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 6812 1.96 - 3.91: 1056 3.91 - 5.86: 76 5.86 - 7.82: 5 7.82 - 9.77: 3 Bond angle restraints: 7952 Sorted by residual: angle pdb=" C ALA A 705 " pdb=" N GLY A 706 " pdb=" CA GLY A 706 " ideal model delta sigma weight residual 120.10 124.17 -4.07 9.50e-01 1.11e+00 1.84e+01 angle pdb=" CB ARG A 213 " pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " ideal model delta sigma weight residual 111.30 121.07 -9.77 2.30e+00 1.89e-01 1.81e+01 angle pdb=" N GLN A 39 " pdb=" CA GLN A 39 " pdb=" C GLN A 39 " ideal model delta sigma weight residual 112.23 107.09 5.14 1.26e+00 6.30e-01 1.67e+01 angle pdb=" C ILE A 771 " pdb=" N ASN A 772 " pdb=" CA ASN A 772 " ideal model delta sigma weight residual 123.46 118.32 5.14 1.35e+00 5.49e-01 1.45e+01 angle pdb=" CA ASP A 118 " pdb=" CB ASP A 118 " pdb=" CG ASP A 118 " ideal model delta sigma weight residual 112.60 116.32 -3.72 1.00e+00 1.00e+00 1.38e+01 ... (remaining 7947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3064 17.53 - 35.07: 280 35.07 - 52.60: 48 52.60 - 70.14: 17 70.14 - 87.67: 3 Dihedral angle restraints: 3412 sinusoidal: 1389 harmonic: 2023 Sorted by residual: dihedral pdb=" CA ASP A 745 " pdb=" C ASP A 745 " pdb=" N SER A 746 " pdb=" CA SER A 746 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLN A 524 " pdb=" C GLN A 524 " pdb=" N GLY A 525 " pdb=" CA GLY A 525 " ideal model delta harmonic sigma weight residual 180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY A 536 " pdb=" C GLY A 536 " pdb=" N LEU A 537 " pdb=" CA LEU A 537 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 435 0.047 - 0.093: 285 0.093 - 0.139: 140 0.139 - 0.186: 44 0.186 - 0.232: 9 Chirality restraints: 913 Sorted by residual: chirality pdb=" CB VAL A 749 " pdb=" CA VAL A 749 " pdb=" CG1 VAL A 749 " pdb=" CG2 VAL A 749 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL A 638 " pdb=" CA VAL A 638 " pdb=" CG1 VAL A 638 " pdb=" CG2 VAL A 638 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE A 597 " pdb=" CA ILE A 597 " pdb=" CG1 ILE A 597 " pdb=" CG2 ILE A 597 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 910 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 551 " 0.036 2.00e-02 2.50e+03 2.93e-02 1.71e+01 pdb=" CG TYR A 551 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 551 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 551 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 551 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 551 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 551 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR A 551 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 615 " 0.032 2.00e-02 2.50e+03 1.99e-02 9.88e+00 pdb=" CG TRP A 615 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 615 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 615 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 615 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 615 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 615 " -0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 615 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 615 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 615 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 647 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C VAL A 647 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL A 647 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 648 " 0.018 2.00e-02 2.50e+03 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 6 2.46 - 3.07: 3714 3.07 - 3.68: 8511 3.68 - 4.29: 13056 4.29 - 4.90: 21506 Nonbonded interactions: 46793 Sorted by model distance: nonbonded pdb=" OD2 ASP A 652 " pdb="ZN ZN A1000 " model vdw 1.853 2.230 nonbonded pdb=" OE2 GLU A 690 " pdb=" NH1 ARG A 725 " model vdw 2.310 3.120 nonbonded pdb=" O LYS A 660 " pdb=" OG1 THR A 663 " model vdw 2.370 3.040 nonbonded pdb=" NH1 ARG A 710 " pdb=" OH TYR A 711 " model vdw 2.404 3.120 nonbonded pdb=" OE1 GLU A 699 " pdb=" NH1 ARG A 747 " model vdw 2.404 3.120 ... (remaining 46788 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: 1.000 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.010 0.179 5825 Z= 0.638 Angle : 1.376 9.774 7954 Z= 0.920 Chirality : 0.072 0.232 913 Planarity : 0.010 0.099 965 Dihedral : 14.341 87.669 2105 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.72 % Favored : 97.00 % Rotamer: Outliers : 0.51 % Allowed : 3.22 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.09 (0.28), residues: 699 helix: -0.45 (0.24), residues: 336 sheet: -0.22 (0.58), residues: 80 loop : -1.06 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG A 753 TYR 0.053 0.010 TYR A 551 PHE 0.037 0.008 PHE A 4 TRP 0.042 0.009 TRP A 515 HIS 0.012 0.004 HIS A 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00969 / 0.63 ( 5822) covalent geometry : angle 1.37520 / 0.92 ( 7952) SS BOND : bond 0.07819 / 4.12 ( 1) SS BOND : angle 2.94261 / 1.68 ( 2) hydrogen bonds : bond 0.12928 / 8.86 ( 321) hydrogen bonds : angle 6.25059 / 4.38 ( 918) metal coordination : bond 0.17693 / 8.87 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.7442 (m-40) cc_final: 0.7070 (m110) REVERT: A 76 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7335 (ttm-80) REVERT: A 88 ASP cc_start: 0.7624 (m-30) cc_final: 0.7266 (p0) REVERT: A 159 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.6989 (ttm170) REVERT: A 169 GLN cc_start: 0.7420 (mt0) cc_final: 0.6640 (mm110) REVERT: A 188 GLN cc_start: 0.8013 (mt0) cc_final: 0.7184 (mp10) REVERT: A 189 GLN cc_start: 0.7081 (mp10) cc_final: 0.6362 (mp10) REVERT: A 207 GLU cc_start: 0.8323 (pm20) cc_final: 0.7882 (pt0) REVERT: A 232 THR cc_start: 0.7697 (m) cc_final: 0.7209 (p) REVERT: A 302 TRP cc_start: 0.6771 (m100) cc_final: 0.6443 (m-90) REVERT: A 411 MET cc_start: 0.6092 (ttp) cc_final: 0.5792 (ttp) REVERT: A 642 ASP cc_start: 0.6627 (t70) cc_final: 0.6350 (p0) REVERT: A 654 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 673 MET cc_start: 0.7854 (mtp) cc_final: 0.7072 (mmt) REVERT: A 697 SER cc_start: 0.8166 (t) cc_final: 0.7897 (m) REVERT: A 748 GLU cc_start: 0.8410 (tt0) cc_final: 0.7739 (tp30) REVERT: A 763 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7047 (mtt-85) outliers start: 3 outliers final: 1 residues processed: 100 average time/residue: 0.4214 time to fit residues: 44.2330 Evaluate side-chains 73 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 664 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119590 restraints weight = 6383.891| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.65 r_work: 0.3205 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5825 Z= 0.148 Angle : 0.607 7.358 7954 Z= 0.319 Chirality : 0.042 0.139 913 Planarity : 0.005 0.049 965 Dihedral : 11.756 78.555 833 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.69 % Allowed : 8.98 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 699 helix: 1.39 (0.26), residues: 338 sheet: -0.14 (0.53), residues: 97 loop : -0.72 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 725 TYR 0.007 0.001 TYR A 38 PHE 0.016 0.002 PHE A 127 TRP 0.034 0.001 TRP A 370 HIS 0.007 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 5822) covalent geometry : angle 0.60717 / 0.32 ( 7952) SS BOND : bond 0.00007 / 0.00 ( 1) SS BOND : angle 0.95738 / 0.52 ( 2) hydrogen bonds : bond 0.04874 / 3.15 ( 321) hydrogen bonds : angle 4.87541 / 3.43 ( 918) metal coordination : bond 0.00757 / 0.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8158 (m-40) cc_final: 0.7904 (m110) REVERT: A 76 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.8198 (ttt90) REVERT: A 188 GLN cc_start: 0.8046 (mt0) cc_final: 0.7502 (mp-120) REVERT: A 189 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: A 302 TRP cc_start: 0.7653 (m100) cc_final: 0.7361 (m-90) REVERT: A 370 TRP cc_start: 0.5771 (p-90) cc_final: 0.5542 (p-90) REVERT: A 411 MET cc_start: 0.7923 (ttp) cc_final: 0.7472 (ttp) REVERT: A 659 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7584 (mpp) outliers start: 10 outliers final: 3 residues processed: 84 average time/residue: 0.4286 time to fit residues: 37.8132 Evaluate side-chains 70 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 659 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 11 optimal weight: 0.0010 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118807 restraints weight = 6341.975| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.65 r_work: 0.3180 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 5825 Z= 0.174 Angle : 0.598 6.823 7954 Z= 0.318 Chirality : 0.042 0.154 913 Planarity : 0.004 0.031 965 Dihedral : 11.508 80.217 832 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.56 % Allowed : 9.66 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.02 (0.31), residues: 699 helix: 1.97 (0.27), residues: 338 sheet: -0.03 (0.52), residues: 95 loop : -0.74 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 213 TYR 0.007 0.001 TYR A 591 PHE 0.017 0.002 PHE A 127 TRP 0.030 0.001 TRP A 370 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 5822) covalent geometry : angle 0.59751 / 0.32 ( 7952) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 0.77234 / 0.43 ( 2) hydrogen bonds : bond 0.04558 / 2.96 ( 321) hydrogen bonds : angle 4.64221 / 3.25 ( 918) metal coordination : bond 0.00141 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.134 Fit side-chains REVERT: A 2 ASN cc_start: 0.8200 (m-40) cc_final: 0.7998 (m110) REVERT: A 188 GLN cc_start: 0.8190 (mt0) cc_final: 0.7651 (mp10) REVERT: A 189 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: A 214 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6901 (tp-100) REVERT: A 302 TRP cc_start: 0.7696 (m100) cc_final: 0.7401 (m-90) REVERT: A 370 TRP cc_start: 0.5731 (p-90) cc_final: 0.5483 (p-90) REVERT: A 396 MET cc_start: 0.8319 (mmt) cc_final: 0.8107 (mmm) REVERT: A 411 MET cc_start: 0.8117 (ttp) cc_final: 0.7652 (ttp) REVERT: A 659 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7546 (mpp) REVERT: A 668 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6465 (mp10) REVERT: A 673 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8179 (mmt) outliers start: 21 outliers final: 9 residues processed: 78 average time/residue: 0.3804 time to fit residues: 31.3007 Evaluate side-chains 75 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 668 GLN Chi-restraints excluded: chain A residue 673 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 395 ASN A 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107949 restraints weight = 6229.387| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.56 r_work: 0.3034 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5825 Z= 0.129 Angle : 0.534 6.488 7954 Z= 0.283 Chirality : 0.041 0.144 913 Planarity : 0.004 0.031 965 Dihedral : 11.282 81.614 832 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.05 % Allowed : 11.02 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.20 (0.31), residues: 699 helix: 2.22 (0.27), residues: 338 sheet: -0.20 (0.50), residues: 92 loop : -0.68 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 763 TYR 0.007 0.001 TYR A 143 PHE 0.017 0.001 PHE A 127 TRP 0.028 0.001 TRP A 370 HIS 0.007 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 5822) covalent geometry : angle 0.53355 / 0.28 ( 7952) SS BOND : bond 0.00071 / 0.04 ( 1) SS BOND : angle 0.56572 / 0.31 ( 2) hydrogen bonds : bond 0.04035 / 2.62 ( 321) hydrogen bonds : angle 4.47067 / 3.12 ( 918) metal coordination : bond 0.00018 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.206 Fit side-chains REVERT: A 189 GLN cc_start: 0.7889 (mp10) cc_final: 0.7556 (mp10) REVERT: A 302 TRP cc_start: 0.7693 (m100) cc_final: 0.7362 (m-90) REVERT: A 370 TRP cc_start: 0.5788 (p-90) cc_final: 0.5505 (p-90) REVERT: A 396 MET cc_start: 0.8367 (mmt) cc_final: 0.8065 (mmm) REVERT: A 411 MET cc_start: 0.8135 (ttp) cc_final: 0.7671 (ttp) REVERT: A 673 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8154 (mmt) outliers start: 18 outliers final: 8 residues processed: 72 average time/residue: 0.2934 time to fit residues: 22.6129 Evaluate side-chains 68 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 673 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.0030 chunk 45 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108352 restraints weight = 6319.576| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.57 r_work: 0.3046 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5825 Z= 0.115 Angle : 0.511 6.306 7954 Z= 0.271 Chirality : 0.040 0.141 913 Planarity : 0.004 0.031 965 Dihedral : 11.085 83.067 832 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.22 % Allowed : 11.53 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.33 (0.31), residues: 699 helix: 2.29 (0.27), residues: 344 sheet: -0.16 (0.51), residues: 92 loop : -0.64 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.008 0.001 TYR A 143 PHE 0.016 0.001 PHE A 127 TRP 0.027 0.001 TRP A 370 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 5822) covalent geometry : angle 0.51093 / 0.27 ( 7952) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 0.47647 / 0.26 ( 2) hydrogen bonds : bond 0.03757 / 2.45 ( 321) hydrogen bonds : angle 4.35624 / 3.03 ( 918) metal coordination : bond 0.00027 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.125 Fit side-chains REVERT: A 189 GLN cc_start: 0.7937 (mp10) cc_final: 0.7414 (mp10) REVERT: A 213 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6102 (ttp-170) REVERT: A 302 TRP cc_start: 0.7612 (m100) cc_final: 0.7326 (m-90) REVERT: A 370 TRP cc_start: 0.5713 (p-90) cc_final: 0.5397 (p-90) REVERT: A 396 MET cc_start: 0.8372 (mmt) cc_final: 0.8072 (mmm) REVERT: A 411 MET cc_start: 0.8128 (ttp) cc_final: 0.7677 (ttp) REVERT: A 428 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7736 (tpp) REVERT: A 659 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7302 (mpp) outliers start: 19 outliers final: 7 residues processed: 74 average time/residue: 0.3681 time to fit residues: 28.8490 Evaluate side-chains 67 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 659 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.146005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107742 restraints weight = 6252.184| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.56 r_work: 0.3035 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5825 Z= 0.134 Angle : 0.530 6.293 7954 Z= 0.279 Chirality : 0.041 0.144 913 Planarity : 0.004 0.032 965 Dihedral : 11.071 83.731 832 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.05 % Allowed : 11.53 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.32 (0.31), residues: 699 helix: 2.30 (0.27), residues: 344 sheet: -0.14 (0.51), residues: 92 loop : -0.68 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 763 TYR 0.006 0.001 TYR A 143 PHE 0.018 0.001 PHE A 127 TRP 0.026 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 5822) covalent geometry : angle 0.53026 / 0.28 ( 7952) SS BOND : bond 0.01525 / 0.80 ( 1) SS BOND : angle 0.94985 / 0.50 ( 2) hydrogen bonds : bond 0.03895 / 2.54 ( 321) hydrogen bonds : angle 4.33874 / 3.01 ( 918) metal coordination : bond 0.00013 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.130 Fit side-chains REVERT: A 188 GLN cc_start: 0.8076 (mt0) cc_final: 0.7622 (mp10) REVERT: A 189 GLN cc_start: 0.7923 (mp10) cc_final: 0.7459 (mp10) REVERT: A 213 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6143 (ttp-170) REVERT: A 285 MET cc_start: 0.8815 (mtm) cc_final: 0.8457 (mtm) REVERT: A 302 TRP cc_start: 0.7628 (m100) cc_final: 0.7338 (m-90) REVERT: A 370 TRP cc_start: 0.5552 (p-90) cc_final: 0.5296 (p-90) REVERT: A 396 MET cc_start: 0.8348 (mmt) cc_final: 0.8044 (mmm) REVERT: A 411 MET cc_start: 0.8114 (ttp) cc_final: 0.7689 (ttp) REVERT: A 428 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7742 (tpp) REVERT: A 673 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8145 (mmt) outliers start: 18 outliers final: 9 residues processed: 69 average time/residue: 0.3238 time to fit residues: 23.7777 Evaluate side-chains 73 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 673 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108362 restraints weight = 6342.215| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.57 r_work: 0.3033 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5825 Z= 0.120 Angle : 0.517 6.296 7954 Z= 0.272 Chirality : 0.040 0.140 913 Planarity : 0.004 0.032 965 Dihedral : 11.003 84.312 832 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.71 % Allowed : 12.71 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.39 (0.31), residues: 699 helix: 2.38 (0.27), residues: 344 sheet: -0.14 (0.51), residues: 92 loop : -0.66 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.007 0.001 TYR A 143 PHE 0.017 0.001 PHE A 127 TRP 0.026 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 5822) covalent geometry : angle 0.51657 / 0.27 ( 7952) SS BOND : bond 0.00129 / 0.07 ( 1) SS BOND : angle 1.51770 / 0.80 ( 2) hydrogen bonds : bond 0.03730 / 2.43 ( 321) hydrogen bonds : angle 4.31753 / 3.00 ( 918) metal coordination : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 72 PRO cc_start: 0.8931 (Cg_exo) cc_final: 0.8729 (Cg_endo) REVERT: A 188 GLN cc_start: 0.8130 (mt0) cc_final: 0.7803 (pt0) REVERT: A 213 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6080 (ttp-170) REVERT: A 302 TRP cc_start: 0.7613 (m100) cc_final: 0.7315 (m-90) REVERT: A 370 TRP cc_start: 0.5534 (p-90) cc_final: 0.5286 (p-90) REVERT: A 396 MET cc_start: 0.8298 (mmt) cc_final: 0.7986 (mmm) REVERT: A 411 MET cc_start: 0.8115 (ttp) cc_final: 0.7710 (ttp) REVERT: A 428 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7718 (tpp) REVERT: A 659 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7390 (mpp) outliers start: 16 outliers final: 9 residues processed: 76 average time/residue: 0.3142 time to fit residues: 25.5259 Evaluate side-chains 75 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 659 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.145345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106753 restraints weight = 6180.760| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.61 r_work: 0.3019 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5825 Z= 0.142 Angle : 0.538 6.190 7954 Z= 0.282 Chirality : 0.041 0.145 913 Planarity : 0.004 0.032 965 Dihedral : 11.041 84.901 832 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.22 % Allowed : 12.71 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.34 (0.31), residues: 699 helix: 2.33 (0.27), residues: 344 sheet: -0.13 (0.51), residues: 92 loop : -0.70 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 763 TYR 0.007 0.001 TYR A 143 PHE 0.019 0.001 PHE A 127 TRP 0.026 0.001 TRP A 370 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5822) covalent geometry : angle 0.53732 / 0.28 ( 7952) SS BOND : bond 0.00412 / 0.22 ( 1) SS BOND : angle 1.06140 / 0.56 ( 2) hydrogen bonds : bond 0.03918 / 2.56 ( 321) hydrogen bonds : angle 4.33786 / 3.00 ( 918) metal coordination : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 72 PRO cc_start: 0.8934 (Cg_exo) cc_final: 0.8730 (Cg_endo) REVERT: A 188 GLN cc_start: 0.8151 (mt0) cc_final: 0.7803 (pt0) REVERT: A 213 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6097 (ttp-170) REVERT: A 239 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7830 (ttm) REVERT: A 302 TRP cc_start: 0.7621 (m100) cc_final: 0.7309 (m-90) REVERT: A 370 TRP cc_start: 0.5451 (p-90) cc_final: 0.5154 (p-90) REVERT: A 396 MET cc_start: 0.8311 (mmt) cc_final: 0.7988 (mmm) REVERT: A 411 MET cc_start: 0.8133 (ttp) cc_final: 0.7719 (ttp) REVERT: A 428 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7697 (tpp) REVERT: A 659 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7367 (mpp) outliers start: 19 outliers final: 9 residues processed: 74 average time/residue: 0.3449 time to fit residues: 26.9902 Evaluate side-chains 77 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 659 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.0060 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN A 86 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.107594 restraints weight = 6262.581| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.56 r_work: 0.3035 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5825 Z= 0.129 Angle : 0.527 6.192 7954 Z= 0.277 Chirality : 0.041 0.143 913 Planarity : 0.004 0.032 965 Dihedral : 11.031 85.186 832 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.05 % Allowed : 13.05 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.38 (0.31), residues: 699 helix: 2.39 (0.27), residues: 344 sheet: -0.14 (0.51), residues: 92 loop : -0.70 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 763 TYR 0.007 0.001 TYR A 143 PHE 0.017 0.001 PHE A 127 TRP 0.027 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5822) covalent geometry : angle 0.52635 / 0.28 ( 7952) SS BOND : bond 0.00306 / 0.16 ( 1) SS BOND : angle 1.12234 / 0.59 ( 2) hydrogen bonds : bond 0.03802 / 2.48 ( 321) hydrogen bonds : angle 4.31260 / 2.99 ( 918) metal coordination : bond 0.00036 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.137 Fit side-chains REVERT: A 72 PRO cc_start: 0.8924 (Cg_exo) cc_final: 0.8721 (Cg_endo) REVERT: A 188 GLN cc_start: 0.8186 (mt0) cc_final: 0.7635 (mp10) REVERT: A 189 GLN cc_start: 0.7977 (mp10) cc_final: 0.7465 (mp10) REVERT: A 213 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6086 (ttp-170) REVERT: A 239 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7788 (ttm) REVERT: A 302 TRP cc_start: 0.7611 (m100) cc_final: 0.7294 (m-90) REVERT: A 370 TRP cc_start: 0.5447 (p-90) cc_final: 0.5191 (p-90) REVERT: A 396 MET cc_start: 0.8293 (mmt) cc_final: 0.7965 (mmm) REVERT: A 411 MET cc_start: 0.8136 (ttp) cc_final: 0.7724 (ttp) REVERT: A 428 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7700 (tpp) REVERT: A 659 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7355 (mpp) outliers start: 18 outliers final: 9 residues processed: 73 average time/residue: 0.3659 time to fit residues: 28.3701 Evaluate side-chains 76 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 659 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 7 optimal weight: 0.0010 chunk 3 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.0060 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN A 395 ASN A 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109333 restraints weight = 6360.907| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.57 r_work: 0.3057 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5825 Z= 0.107 Angle : 0.507 6.298 7954 Z= 0.267 Chirality : 0.040 0.138 913 Planarity : 0.003 0.033 965 Dihedral : 10.954 85.476 832 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.03 % Allowed : 14.24 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.49 (0.32), residues: 699 helix: 2.49 (0.27), residues: 344 sheet: -0.13 (0.51), residues: 91 loop : -0.66 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 763 TYR 0.007 0.001 TYR A 143 PHE 0.018 0.001 PHE A 404 TRP 0.028 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 5822) covalent geometry : angle 0.50649 / 0.27 ( 7952) SS BOND : bond 0.00223 / 0.12 ( 1) SS BOND : angle 0.98463 / 0.52 ( 2) hydrogen bonds : bond 0.03506 / 2.26 ( 321) hydrogen bonds : angle 4.25771 / 2.96 ( 918) metal coordination : bond 0.00014 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.137 Fit side-chains REVERT: A 188 GLN cc_start: 0.8173 (mt0) cc_final: 0.7677 (mp10) REVERT: A 189 GLN cc_start: 0.7984 (mp10) cc_final: 0.7694 (mp10) REVERT: A 213 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6291 (ttp-170) REVERT: A 239 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7808 (ttm) REVERT: A 302 TRP cc_start: 0.7632 (m100) cc_final: 0.7339 (m-90) REVERT: A 396 MET cc_start: 0.8284 (mmt) cc_final: 0.7937 (mmm) REVERT: A 411 MET cc_start: 0.8144 (ttp) cc_final: 0.7756 (ttp) REVERT: A 428 MET cc_start: 0.7923 (mmm) cc_final: 0.7706 (tpp) outliers start: 12 outliers final: 6 residues processed: 73 average time/residue: 0.3636 time to fit residues: 28.2314 Evaluate side-chains 73 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 656 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN A 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109069 restraints weight = 6279.747| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.56 r_work: 0.3051 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5825 Z= 0.113 Angle : 0.520 7.451 7954 Z= 0.272 Chirality : 0.040 0.145 913 Planarity : 0.004 0.033 965 Dihedral : 10.974 85.773 832 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.03 % Allowed : 14.75 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.48 (0.32), residues: 699 helix: 2.49 (0.27), residues: 344 sheet: -0.13 (0.51), residues: 91 loop : -0.66 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 763 TYR 0.007 0.001 TYR A 143 PHE 0.018 0.001 PHE A 404 TRP 0.053 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 5822) covalent geometry : angle 0.51967 / 0.27 ( 7952) SS BOND : bond 0.00272 / 0.14 ( 1) SS BOND : angle 1.00397 / 0.53 ( 2) hydrogen bonds : bond 0.03561 / 2.31 ( 321) hydrogen bonds : angle 4.22605 / 2.94 ( 918) metal coordination : bond 0.00017 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.13 seconds wall clock time: 29 minutes 30.77 seconds (1770.77 seconds total)