Starting phenix.real_space_refine on Wed Jun 3 13:56:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vcf_64953/06_2026/9vcf_64953.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vcf_64953/06_2026/9vcf_64953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vcf_64953/06_2026/9vcf_64953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vcf_64953/06_2026/9vcf_64953.map" model { file = "/net/cci-nas-00/data/ceres_data/9vcf_64953/06_2026/9vcf_64953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vcf_64953/06_2026/9vcf_64953.cif" } resolution = 3.23 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= 0.016 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 29 5.49 5 S 23 5.16 5 C 3899 2.51 5 N 1046 2.21 5 O 1114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6112 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5515 Classifications: {'peptide': 704} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 666} Chain breaks: 2 Chain: "B" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 311 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} 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: 1.45, per 1000 atoms: 0.24 Number of scatterers: 6112 At special positions: 0 Unit cell: (90.7494, 76.3623, 117.31, 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 29 15.00 O 1114 8.00 N 1046 7.00 C 3899 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=2.05 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: 0.54 Conformation dependent library (CDL) restraints added in 290.7 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 " 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1302 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 56.4% alpha, 15.2% beta 13 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 0.75 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 198 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.068A 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 251 through 273 removed outlier: 4.286A pdb=" N TRP A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) 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 341 removed outlier: 3.772A pdb=" N TRP A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 384 Processing helix chain 'A' and resid 388 through 405 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 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: 3.590A pdb=" N GLU A 658 " --> pdb=" O GLU A 654 " (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 725 removed outlier: 3.696A pdb=" N ARG A 725 " --> pdb=" O ARG A 721 " (cutoff:3.500A) 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 165 through 167 removed outlier: 6.335A pdb=" N LEU A 165 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 126 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR A 130 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL A 160 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 132 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLY A 158 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS A 108 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLY A 158 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 110 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 160 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR A 112 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LYS A 162 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N LYS A 114 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TRP A 89 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER A 84 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER A 91 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU A 82 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP A 93 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 595 through 598 removed outlier: 9.602A pdb=" N GLN A 595 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP A 569 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE A 597 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 571 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY A 536 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N PHE A 572 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 538 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 611 through 615 removed outlier: 6.685A pdb=" N VAL A 637 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG A 646 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE A 678 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 648 " --> pdb=" O ILE A 678 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 1442 1.34 - 1.47: 2139 1.47 - 1.61: 2686 1.61 - 1.75: 17 1.75 - 1.88: 39 Bond restraints: 6323 Sorted by residual: bond pdb=" CA SER A 229 " pdb=" CB SER A 229 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.59e-02 3.96e+03 1.79e+01 bond pdb=" CA SER A 20 " pdb=" CB SER A 20 " ideal model delta sigma weight residual 1.532 1.466 0.066 1.68e-02 3.54e+03 1.55e+01 bond pdb=" C VAL A 529 " pdb=" O VAL A 529 " ideal model delta sigma weight residual 1.238 1.198 0.039 1.10e-02 8.26e+03 1.27e+01 bond pdb=" CA SER A 674 " pdb=" CB SER A 674 " ideal model delta sigma weight residual 1.534 1.475 0.058 1.78e-02 3.16e+03 1.07e+01 bond pdb=" CG MET A 411 " pdb=" SD MET A 411 " ideal model delta sigma weight residual 1.803 1.883 -0.080 2.50e-02 1.60e+03 1.03e+01 ... (remaining 6318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 7568 1.96 - 3.92: 1056 3.92 - 5.88: 89 5.88 - 7.84: 9 7.84 - 9.80: 2 Bond angle restraints: 8724 Sorted by residual: angle pdb=" C PRO A 19 " pdb=" CA PRO A 19 " pdb=" CB PRO A 19 " ideal model delta sigma weight residual 112.64 104.64 8.00 1.74e+00 3.30e-01 2.12e+01 angle pdb=" CG ARG A 747 " pdb=" CD ARG A 747 " pdb=" NE ARG A 747 " ideal model delta sigma weight residual 112.00 102.20 9.80 2.20e+00 2.07e-01 1.98e+01 angle pdb=" CA ASP A 641 " pdb=" CB ASP A 641 " pdb=" CG ASP A 641 " ideal model delta sigma weight residual 112.60 117.04 -4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" N ALA A 270 " pdb=" CA ALA A 270 " pdb=" C ALA A 270 " ideal model delta sigma weight residual 111.36 106.71 4.65 1.09e+00 8.42e-01 1.82e+01 angle pdb=" N TYR A 551 " pdb=" CA TYR A 551 " pdb=" C TYR A 551 " ideal model delta sigma weight residual 113.01 107.91 5.10 1.20e+00 6.94e-01 1.80e+01 ... (remaining 8719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 3016 14.26 - 28.51: 388 28.51 - 42.77: 133 42.77 - 57.02: 89 57.02 - 71.28: 12 Dihedral angle restraints: 3638 sinusoidal: 1618 harmonic: 2020 Sorted by residual: dihedral pdb=" CA ARG A 63 " pdb=" C ARG A 63 " pdb=" N GLN A 64 " pdb=" CA GLN A 64 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LEU A 770 " pdb=" C LEU A 770 " pdb=" N ILE A 771 " pdb=" CA ILE A 771 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA GLN A 64 " pdb=" C GLN A 64 " pdb=" N ASP A 65 " pdb=" CA ASP A 65 " ideal model delta harmonic sigma weight residual -180.00 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 3635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 482 0.044 - 0.088: 319 0.088 - 0.131: 149 0.131 - 0.175: 41 0.175 - 0.219: 9 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CB ILE A 603 " pdb=" CA ILE A 603 " pdb=" CG1 ILE A 603 " pdb=" CG2 ILE A 603 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE A 568 " pdb=" CA ILE A 568 " pdb=" CG1 ILE A 568 " pdb=" CG2 ILE A 568 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA SER A 62 " pdb=" N SER A 62 " pdb=" C SER A 62 " pdb=" CB SER A 62 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 997 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 49 " 0.050 2.00e-02 2.50e+03 3.13e-02 1.71e+01 pdb=" CG PHE A 49 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 49 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 49 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 49 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 49 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 49 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 18 " -0.005 2.00e-02 2.50e+03 2.25e-02 1.26e+01 pdb=" CG TRP A 18 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 18 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 18 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 18 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP A 18 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 18 " -0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 18 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 18 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 18 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 737 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C GLN A 737 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN A 737 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE A 738 " 0.018 2.00e-02 2.50e+03 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 6 2.41 - 3.03: 3603 3.03 - 3.66: 9323 3.66 - 4.28: 14356 4.28 - 4.90: 23384 Nonbonded interactions: 50672 Sorted by model distance: nonbonded pdb=" OD2 ASP A 652 " pdb="ZN ZN A1000 " model vdw 1.791 2.230 nonbonded pdb=" O LYS A 660 " pdb=" OG1 THR A 663 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 539 " pdb=" O CYS A 636 " model vdw 2.312 3.040 nonbonded pdb=" NZ LYS A 108 " pdb=" O GLN A 152 " model vdw 2.336 3.120 nonbonded pdb=" O ARG A 63 " pdb=" NH2 ARG A 104 " model vdw 2.384 3.120 ... (remaining 50667 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: 1.080 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.430 Find NCS groups from input model: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 0.080 6326 Z= 0.608 Angle : 1.349 9.801 8726 Z= 0.902 Chirality : 0.068 0.219 1000 Planarity : 0.008 0.031 986 Dihedral : 16.780 71.277 2333 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.68 % Allowed : 3.90 % Favored : 95.42 % 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: -0.46 (0.27), residues: 698 helix: 0.53 (0.24), residues: 335 sheet: -0.29 (0.58), residues: 69 loop : -1.23 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG A 639 TYR 0.037 0.008 TYR A 236 PHE 0.050 0.009 PHE A 49 TRP 0.044 0.008 TRP A 18 HIS 0.017 0.004 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00964 / 0.61 ( 6323) covalent geometry : angle 1.34861 / 0.90 ( 8724) SS BOND : bond 0.01416 / 0.75 ( 1) SS BOND : angle 1.60733 / 0.88 ( 2) hydrogen bonds : bond 0.15268 / 10.57 ( 355) hydrogen bonds : angle 6.37360 / 4.65 ( 985) metal coordination : bond 0.06056 / 3.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 89 TRP cc_start: 0.7333 (p-90) cc_final: 0.7094 (p-90) REVERT: A 167 GLU cc_start: 0.8320 (tt0) cc_final: 0.7906 (mt-10) REVERT: A 566 ARG cc_start: 0.8457 (mpp80) cc_final: 0.7931 (mmt180) REVERT: A 593 LYS cc_start: 0.8039 (mttt) cc_final: 0.7629 (tttp) REVERT: A 671 ILE cc_start: 0.8396 (tt) cc_final: 0.8031 (tp) REVERT: A 720 ASP cc_start: 0.8336 (m-30) cc_final: 0.8069 (m-30) outliers start: 4 outliers final: 0 residues processed: 105 average time/residue: 0.1012 time to fit residues: 13.5658 Evaluate side-chains 70 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 189 GLN A 664 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.163362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.112260 restraints weight = 6107.305| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.67 r_work: 0.2959 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6326 Z= 0.145 Angle : 0.580 6.300 8726 Z= 0.306 Chirality : 0.040 0.143 1000 Planarity : 0.004 0.029 986 Dihedral : 18.648 80.315 1060 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.85 % Allowed : 7.12 % Favored : 92.03 % 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: 0.91 (0.29), residues: 698 helix: 2.02 (0.25), residues: 338 sheet: -0.32 (0.58), residues: 61 loop : -0.87 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 766 TYR 0.008 0.001 TYR A 143 PHE 0.023 0.002 PHE A 378 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 6323) covalent geometry : angle 0.57991 / 0.31 ( 8724) SS BOND : bond 0.00280 / 0.15 ( 1) SS BOND : angle 0.52721 / 0.29 ( 2) hydrogen bonds : bond 0.04339 / 2.91 ( 355) hydrogen bonds : angle 4.22730 / 3.08 ( 985) metal coordination : bond 0.00197 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.219 Fit side-chains REVERT: A 167 GLU cc_start: 0.7989 (tt0) cc_final: 0.7585 (mt-10) REVERT: A 214 GLN cc_start: 0.6523 (pp30) cc_final: 0.6003 (tm-30) REVERT: A 239 MET cc_start: 0.7575 (mmp) cc_final: 0.7371 (mmp) REVERT: A 566 ARG cc_start: 0.8159 (mpp80) cc_final: 0.7836 (mmt180) REVERT: A 593 LYS cc_start: 0.8011 (mttt) cc_final: 0.7646 (ptmt) REVERT: A 720 ASP cc_start: 0.7944 (m-30) cc_final: 0.7547 (m-30) REVERT: A 763 ARG cc_start: 0.7992 (mmt-90) cc_final: 0.7471 (mmt90) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.1008 time to fit residues: 9.9631 Evaluate side-chains 65 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 514 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN ** A 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.168457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.126056 restraints weight = 6022.130| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.36 r_work: 0.2924 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6326 Z= 0.148 Angle : 0.557 5.823 8726 Z= 0.290 Chirality : 0.040 0.146 1000 Planarity : 0.004 0.027 986 Dihedral : 18.589 77.765 1060 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.19 % Allowed : 10.00 % Favored : 88.81 % 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: 1.35 (0.30), residues: 698 helix: 2.57 (0.26), residues: 339 sheet: -0.38 (0.58), residues: 61 loop : -0.84 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 766 TYR 0.010 0.001 TYR A 143 PHE 0.018 0.001 PHE A 378 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6323) covalent geometry : angle 0.55690 / 0.29 ( 8724) SS BOND : bond 0.00154 / 0.08 ( 1) SS BOND : angle 0.39316 / 0.21 ( 2) hydrogen bonds : bond 0.04158 / 2.80 ( 355) hydrogen bonds : angle 4.05715 / 2.97 ( 985) metal coordination : bond 0.00262 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.197 Fit side-chains REVERT: A 76 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8087 (ttp80) REVERT: A 89 TRP cc_start: 0.7591 (p-90) cc_final: 0.7113 (p90) REVERT: A 167 GLU cc_start: 0.8199 (tt0) cc_final: 0.7868 (mt-10) REVERT: A 211 MET cc_start: 0.6563 (ttt) cc_final: 0.6243 (ttt) REVERT: A 214 GLN cc_start: 0.6620 (pp30) cc_final: 0.6114 (pp30) REVERT: A 372 LEU cc_start: 0.8391 (mp) cc_final: 0.8089 (mp) REVERT: A 593 LYS cc_start: 0.8130 (mttt) cc_final: 0.7859 (ptmt) REVERT: A 671 ILE cc_start: 0.8885 (tt) cc_final: 0.8501 (tp) REVERT: A 678 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8342 (mm) REVERT: A 720 ASP cc_start: 0.8071 (m-30) cc_final: 0.7749 (m-30) REVERT: A 763 ARG cc_start: 0.8321 (mmt-90) cc_final: 0.7852 (mmt90) outliers start: 7 outliers final: 3 residues processed: 76 average time/residue: 0.0861 time to fit residues: 8.5754 Evaluate side-chains 70 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 678 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 29 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.172262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132440 restraints weight = 5991.489| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.24 r_work: 0.2964 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6326 Z= 0.117 Angle : 0.510 6.051 8726 Z= 0.268 Chirality : 0.039 0.139 1000 Planarity : 0.003 0.026 986 Dihedral : 18.615 77.865 1060 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.02 % Allowed : 12.03 % Favored : 86.95 % 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 (0.31), residues: 698 helix: 2.69 (0.26), residues: 344 sheet: -0.25 (0.59), residues: 61 loop : -0.86 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 766 TYR 0.008 0.001 TYR A 143 PHE 0.012 0.001 PHE A 8 TRP 0.009 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6323) covalent geometry : angle 0.51044 / 0.27 ( 8724) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 0.34165 / 0.18 ( 2) hydrogen bonds : bond 0.03611 / 2.41 ( 355) hydrogen bonds : angle 3.89847 / 2.86 ( 985) metal coordination : bond 0.00188 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.216 Fit side-chains REVERT: A 76 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8090 (ttp80) REVERT: A 167 GLU cc_start: 0.8127 (tt0) cc_final: 0.7828 (mt-10) REVERT: A 211 MET cc_start: 0.6863 (ttt) cc_final: 0.6490 (ttt) REVERT: A 214 GLN cc_start: 0.6564 (pp30) cc_final: 0.6020 (pp30) REVERT: A 372 LEU cc_start: 0.8383 (mp) cc_final: 0.8135 (mp) REVERT: A 411 MET cc_start: 0.7053 (mmm) cc_final: 0.5434 (ptt) REVERT: A 593 LYS cc_start: 0.8163 (mttt) cc_final: 0.7851 (ptmt) REVERT: A 652 ASP cc_start: 0.8416 (m-30) cc_final: 0.7983 (m-30) REVERT: A 671 ILE cc_start: 0.8852 (tt) cc_final: 0.8461 (tp) REVERT: A 720 ASP cc_start: 0.8038 (m-30) cc_final: 0.7743 (m-30) REVERT: A 763 ARG cc_start: 0.8238 (mmt-90) cc_final: 0.7769 (mmt90) outliers start: 6 outliers final: 3 residues processed: 75 average time/residue: 0.0903 time to fit residues: 8.9236 Evaluate side-chains 68 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 608 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 71 optimal weight: 10.0000 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.159537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.105985 restraints weight = 6169.301| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.69 r_work: 0.2903 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.122 Angle : 0.505 6.304 8726 Z= 0.262 Chirality : 0.038 0.138 1000 Planarity : 0.003 0.027 986 Dihedral : 18.657 79.447 1060 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.36 % Allowed : 12.20 % Favored : 86.44 % 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: 1.67 (0.31), residues: 698 helix: 2.91 (0.27), residues: 340 sheet: -0.23 (0.59), residues: 61 loop : -0.82 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.008 0.001 TYR A 143 PHE 0.012 0.001 PHE A 8 TRP 0.008 0.001 TRP A 234 HIS 0.003 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6323) covalent geometry : angle 0.50494 / 0.26 ( 8724) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 0.30696 / 0.16 ( 2) hydrogen bonds : bond 0.03587 / 2.40 ( 355) hydrogen bonds : angle 3.84644 / 2.83 ( 985) metal coordination : bond 0.00185 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 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: 8 poor density : 73 time to evaluate : 0.171 Fit side-chains REVERT: A 76 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8139 (ttp80) REVERT: A 167 GLU cc_start: 0.8200 (tt0) cc_final: 0.7802 (mt-10) REVERT: A 211 MET cc_start: 0.7177 (ttt) cc_final: 0.6584 (mtp) REVERT: A 214 GLN cc_start: 0.6491 (pp30) cc_final: 0.5877 (pp30) REVERT: A 372 LEU cc_start: 0.8306 (mp) cc_final: 0.8063 (mp) REVERT: A 411 MET cc_start: 0.7143 (mmm) cc_final: 0.5347 (ptt) REVERT: A 593 LYS cc_start: 0.8329 (mttt) cc_final: 0.7850 (ptmt) REVERT: A 671 ILE cc_start: 0.8878 (tt) cc_final: 0.8419 (tp) REVERT: A 720 ASP cc_start: 0.8096 (m-30) cc_final: 0.7829 (m-30) REVERT: A 763 ARG cc_start: 0.8290 (mmt-90) cc_final: 0.7789 (mmt90) outliers start: 8 outliers final: 5 residues processed: 77 average time/residue: 0.0827 time to fit residues: 8.4688 Evaluate side-chains 75 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 608 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 16 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.171216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.129024 restraints weight = 5970.568| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.30 r_work: 0.2970 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.109 Angle : 0.488 6.433 8726 Z= 0.254 Chirality : 0.038 0.136 1000 Planarity : 0.003 0.027 986 Dihedral : 18.612 79.885 1060 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.19 % Allowed : 13.73 % Favored : 85.08 % 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: 1.79 (0.31), residues: 698 helix: 2.98 (0.27), residues: 341 sheet: -0.05 (0.58), residues: 63 loop : -0.75 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.006 0.001 TYR A 143 PHE 0.012 0.001 PHE A 8 TRP 0.009 0.001 TRP A 370 HIS 0.004 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 6323) covalent geometry : angle 0.48828 / 0.25 ( 8724) SS BOND : bond 0.00104 / 0.05 ( 1) SS BOND : angle 0.34504 / 0.18 ( 2) hydrogen bonds : bond 0.03321 / 2.23 ( 355) hydrogen bonds : angle 3.74490 / 2.76 ( 985) metal coordination : bond 0.00126 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8116 (ttp80) REVERT: A 167 GLU cc_start: 0.8089 (tt0) cc_final: 0.7775 (mt-10) REVERT: A 372 LEU cc_start: 0.8472 (mp) cc_final: 0.8267 (mp) REVERT: A 411 MET cc_start: 0.7249 (mmm) cc_final: 0.5536 (ptt) REVERT: A 593 LYS cc_start: 0.8278 (mttt) cc_final: 0.7936 (ptmt) REVERT: A 678 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8301 (mm) REVERT: A 720 ASP cc_start: 0.7996 (m-30) cc_final: 0.7742 (m-30) REVERT: A 763 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7737 (mmt90) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.0900 time to fit residues: 9.4723 Evaluate side-chains 74 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 678 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.171081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.129749 restraints weight = 6031.491| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.69 r_work: 0.2915 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.138 Angle : 0.516 6.810 8726 Z= 0.265 Chirality : 0.038 0.136 1000 Planarity : 0.003 0.027 986 Dihedral : 18.653 79.912 1060 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.19 % Allowed : 14.58 % Favored : 84.24 % 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: 1.76 (0.31), residues: 698 helix: 2.95 (0.27), residues: 341 sheet: -0.19 (0.59), residues: 61 loop : -0.73 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.009 0.001 TYR A 143 PHE 0.012 0.001 PHE A 8 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6323) covalent geometry : angle 0.51609 / 0.26 ( 8724) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.30219 / 0.16 ( 2) hydrogen bonds : bond 0.03607 / 2.41 ( 355) hydrogen bonds : angle 3.82098 / 2.80 ( 985) metal coordination : bond 0.00245 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 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: 7 poor density : 74 time to evaluate : 0.228 Fit side-chains REVERT: A 167 GLU cc_start: 0.8113 (tt0) cc_final: 0.7820 (mt-10) REVERT: A 211 MET cc_start: 0.6660 (ttt) cc_final: 0.6283 (ttt) REVERT: A 214 GLN cc_start: 0.6521 (pp30) cc_final: 0.5936 (pp30) REVERT: A 411 MET cc_start: 0.7312 (mmm) cc_final: 0.5521 (ptt) REVERT: A 593 LYS cc_start: 0.8310 (mttt) cc_final: 0.7924 (ptmt) REVERT: A 671 ILE cc_start: 0.8871 (tt) cc_final: 0.8433 (tp) REVERT: A 678 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8334 (mm) REVERT: A 720 ASP cc_start: 0.7977 (m-30) cc_final: 0.7751 (m-30) REVERT: A 763 ARG cc_start: 0.8252 (mmt-90) cc_final: 0.7772 (mmt90) outliers start: 7 outliers final: 6 residues processed: 78 average time/residue: 0.0838 time to fit residues: 8.7267 Evaluate side-chains 78 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 678 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.170013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.128531 restraints weight = 6057.138| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.63 r_work: 0.2935 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6326 Z= 0.147 Angle : 0.527 7.301 8726 Z= 0.269 Chirality : 0.039 0.137 1000 Planarity : 0.003 0.028 986 Dihedral : 18.717 80.511 1060 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.53 % Allowed : 14.75 % 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: 1.68 (0.31), residues: 698 helix: 2.91 (0.27), residues: 340 sheet: -0.29 (0.59), residues: 61 loop : -0.77 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.009 0.001 TYR A 143 PHE 0.013 0.001 PHE A 8 TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 6323) covalent geometry : angle 0.52701 / 0.27 ( 8724) SS BOND : bond 0.00107 / 0.06 ( 1) SS BOND : angle 0.24350 / 0.13 ( 2) hydrogen bonds : bond 0.03683 / 2.46 ( 355) hydrogen bonds : angle 3.84833 / 2.83 ( 985) metal coordination : bond 0.00278 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 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: 9 poor density : 73 time to evaluate : 0.221 Fit side-chains REVERT: A 167 GLU cc_start: 0.8138 (tt0) cc_final: 0.7876 (mt-10) REVERT: A 211 MET cc_start: 0.6774 (ttt) cc_final: 0.6553 (ttt) REVERT: A 214 GLN cc_start: 0.6560 (pp30) cc_final: 0.6030 (pp30) REVERT: A 411 MET cc_start: 0.7452 (mmm) cc_final: 0.5788 (ptt) REVERT: A 593 LYS cc_start: 0.8296 (mttt) cc_final: 0.7963 (ptmt) REVERT: A 642 ASP cc_start: 0.6709 (p0) cc_final: 0.6204 (p0) REVERT: A 671 ILE cc_start: 0.8940 (tt) cc_final: 0.8554 (tp) REVERT: A 678 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8602 (mm) REVERT: A 720 ASP cc_start: 0.7961 (m-30) cc_final: 0.7752 (m-30) REVERT: A 763 ARG cc_start: 0.8310 (mmt-90) cc_final: 0.7887 (mmt90) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.0833 time to fit residues: 8.6816 Evaluate side-chains 79 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 678 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.158638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.104681 restraints weight = 6214.312| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.70 r_work: 0.2871 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.136 Angle : 0.518 8.143 8726 Z= 0.264 Chirality : 0.038 0.136 1000 Planarity : 0.003 0.030 986 Dihedral : 18.726 82.719 1060 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.36 % Allowed : 15.08 % Favored : 83.56 % 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: 1.71 (0.31), residues: 698 helix: 2.91 (0.27), residues: 341 sheet: -0.36 (0.58), residues: 61 loop : -0.73 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.008 0.001 TYR A 143 PHE 0.013 0.001 PHE A 8 TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 6323) covalent geometry : angle 0.51854 / 0.26 ( 8724) SS BOND : bond 0.00093 / 0.05 ( 1) SS BOND : angle 0.30241 / 0.16 ( 2) hydrogen bonds : bond 0.03569 / 2.38 ( 355) hydrogen bonds : angle 3.82028 / 2.81 ( 985) metal coordination : bond 0.00228 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 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: 8 poor density : 72 time to evaluate : 0.197 Fit side-chains REVERT: A 167 GLU cc_start: 0.8210 (tt0) cc_final: 0.7808 (mt-10) REVERT: A 214 GLN cc_start: 0.6541 (pp30) cc_final: 0.5981 (pp30) REVERT: A 411 MET cc_start: 0.7367 (mmm) cc_final: 0.5561 (ptt) REVERT: A 593 LYS cc_start: 0.8377 (mttt) cc_final: 0.7924 (ptmt) REVERT: A 652 ASP cc_start: 0.8468 (m-30) cc_final: 0.7994 (m-30) REVERT: A 671 ILE cc_start: 0.8892 (tt) cc_final: 0.8520 (tp) REVERT: A 678 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8599 (mm) REVERT: A 720 ASP cc_start: 0.8021 (m-30) cc_final: 0.7808 (m-30) REVERT: A 763 ARG cc_start: 0.8296 (mmt-90) cc_final: 0.7824 (mmt90) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.0845 time to fit residues: 8.5523 Evaluate side-chains 77 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 678 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.171351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132839 restraints weight = 6077.104| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.21 r_work: 0.2948 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6326 Z= 0.124 Angle : 0.508 7.969 8726 Z= 0.260 Chirality : 0.038 0.136 1000 Planarity : 0.003 0.033 986 Dihedral : 18.716 83.958 1060 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.36 % Allowed : 15.59 % Favored : 83.05 % 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: 1.77 (0.31), residues: 698 helix: 2.95 (0.27), residues: 341 sheet: -0.31 (0.58), residues: 61 loop : -0.69 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.007 0.001 TYR A 143 PHE 0.012 0.001 PHE A 8 TRP 0.009 0.001 TRP A 370 HIS 0.004 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 6323) covalent geometry : angle 0.50793 / 0.26 ( 8724) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.32788 / 0.17 ( 2) hydrogen bonds : bond 0.03444 / 2.29 ( 355) hydrogen bonds : angle 3.78172 / 2.78 ( 985) metal coordination : bond 0.00177 / 0.09 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 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: 8 poor density : 72 time to evaluate : 0.217 Fit side-chains REVERT: A 76 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.8165 (ttp80) REVERT: A 167 GLU cc_start: 0.8101 (tt0) cc_final: 0.7768 (mt-10) REVERT: A 214 GLN cc_start: 0.6517 (pp30) cc_final: 0.5951 (pp30) REVERT: A 411 MET cc_start: 0.7296 (mmm) cc_final: 0.5599 (ptt) REVERT: A 593 LYS cc_start: 0.8294 (mttt) cc_final: 0.7964 (ptmt) REVERT: A 671 ILE cc_start: 0.8883 (tt) cc_final: 0.8498 (tp) REVERT: A 678 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8328 (mm) REVERT: A 763 ARG cc_start: 0.8218 (mmt-90) cc_final: 0.7767 (mmt90) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.0857 time to fit residues: 8.7020 Evaluate side-chains 77 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 678 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.0050 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112469 restraints weight = 6167.210| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.62 r_work: 0.2937 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.138 Angle : 0.524 8.310 8726 Z= 0.267 Chirality : 0.038 0.135 1000 Planarity : 0.003 0.032 986 Dihedral : 18.741 84.324 1060 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.36 % Allowed : 15.42 % 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: 1.69 (0.32), residues: 698 helix: 2.91 (0.27), residues: 341 sheet: -0.46 (0.58), residues: 63 loop : -0.73 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 766 TYR 0.008 0.001 TYR A 143 PHE 0.012 0.001 PHE A 8 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6323) covalent geometry : angle 0.52407 / 0.27 ( 8724) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.28367 / 0.15 ( 2) hydrogen bonds : bond 0.03541 / 2.36 ( 355) hydrogen bonds : angle 3.78738 / 2.78 ( 985) metal coordination : bond 0.00234 / 0.12 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1928.21 seconds wall clock time: 33 minutes 40.81 seconds (2020.81 seconds total)