Starting phenix.real_space_refine on Thu Jul 2 03:23:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vcf_64953/07_2026/9vcf_64953.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vcf_64953/07_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_64953/07_2026/9vcf_64953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vcf_64953/07_2026/9vcf_64953.map" model { file = "/net/cci-nas-00/data/ceres_data/9vcf_64953/07_2026/9vcf_64953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vcf_64953/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.49, 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 326.6 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: 0.48 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: 0.96 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: 7570 1.96 - 3.92: 1049 3.92 - 5.88: 94 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: 459 0.044 - 0.088: 329 0.088 - 0.132: 162 0.132 - 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.840 Find NCS groups from input model: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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= 0.613 Angle : 1.347 9.801 8726 Z= 0.907 Chirality : 0.069 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 0.00958 / 0.61 ( 6323) covalent geometry : angle 1.34723 / 0.91 ( 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 : 0.194 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: 0.0836 time to fit residues: 11.4852 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 : 0.156 ------------------------------------------------------------------------------- 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... 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 = 0.3764 r_free = 0.3764 target = 0.161984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.110519 restraints weight = 6103.029| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.65 r_work: 0.2933 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6326 Z= 0.157 Angle : 0.625 5.871 8726 Z= 0.333 Chirality : 0.044 0.193 1000 Planarity : 0.004 0.031 986 Dihedral : 18.610 73.928 1060 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.68 % Allowed : 7.29 % 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: 0.94 (0.29), residues: 698 helix: 2.03 (0.26), residues: 338 sheet: -0.29 (0.58), residues: 61 loop : -0.84 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 747 TYR 0.009 0.001 TYR A 551 PHE 0.018 0.001 PHE A 378 TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 6323) covalent geometry : angle 0.62469 / 0.33 ( 8724) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 0.63387 / 0.36 ( 2) hydrogen bonds : bond 0.05346 / 3.67 ( 355) hydrogen bonds : angle 4.41845 / 3.22 ( 985) metal coordination : bond 0.00486 / 0.23 ( 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 76 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.213 Fit side-chains REVERT: A 167 GLU cc_start: 0.8033 (tt0) cc_final: 0.7729 (mt-10) REVERT: A 214 GLN cc_start: 0.6445 (pp30) cc_final: 0.5991 (tm-30) REVERT: A 239 MET cc_start: 0.7622 (mmp) cc_final: 0.7411 (mmp) REVERT: A 566 ARG cc_start: 0.8176 (mpp80) cc_final: 0.7911 (mmt180) REVERT: A 593 LYS cc_start: 0.8026 (mttt) cc_final: 0.7700 (ptmt) REVERT: A 671 ILE cc_start: 0.8697 (tt) cc_final: 0.8298 (tp) REVERT: A 720 ASP cc_start: 0.7855 (m-30) cc_final: 0.7493 (m-30) REVERT: A 763 ARG cc_start: 0.7995 (mmt-90) cc_final: 0.7494 (mmt90) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.0919 time to fit residues: 8.9389 Evaluate side-chains 63 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 336 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 71 optimal weight: 50.0000 chunk 51 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 664 GLN A 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.126856 restraints weight = 6031.729| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.35 r_work: 0.2923 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6326 Z= 0.137 Angle : 0.570 6.199 8726 Z= 0.301 Chirality : 0.042 0.158 1000 Planarity : 0.004 0.028 986 Dihedral : 18.861 77.749 1060 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.85 % Allowed : 9.15 % Favored : 90.00 % 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: 1.31 (0.30), residues: 698 helix: 2.51 (0.26), residues: 339 sheet: -0.35 (0.59), residues: 61 loop : -0.84 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 766 TYR 0.009 0.001 TYR A 143 PHE 0.021 0.001 PHE A 378 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 0.00307 / 0.14 ( 6323) covalent geometry : angle 0.56971 / 0.30 ( 8724) SS BOND : bond 0.00098 / 0.05 ( 1) SS BOND : angle 0.48487 / 0.26 ( 2) hydrogen bonds : bond 0.04482 / 3.03 ( 355) hydrogen bonds : angle 4.10472 / 3.00 ( 985) metal coordination : bond 0.00377 / 0.19 ( 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 73 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.150 Fit side-chains REVERT: A 167 GLU cc_start: 0.8081 (tt0) cc_final: 0.7766 (mt-10) REVERT: A 214 GLN cc_start: 0.6494 (pp30) cc_final: 0.6121 (pp30) REVERT: A 671 ILE cc_start: 0.8853 (tt) cc_final: 0.8461 (tp) REVERT: A 720 ASP cc_start: 0.8058 (m-30) cc_final: 0.7707 (m-30) REVERT: A 763 ARG cc_start: 0.8172 (mmt-90) cc_final: 0.7757 (mmt90) outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.0703 time to fit residues: 6.9364 Evaluate side-chains 67 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 514 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.0170 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 29 optimal weight: 0.0020 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN A 219 HIS A 395 ASN A 664 GLN A 726 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.170775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.127803 restraints weight = 6029.046| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.40 r_work: 0.2944 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6326 Z= 0.114 Angle : 0.529 5.782 8726 Z= 0.280 Chirality : 0.040 0.129 1000 Planarity : 0.004 0.027 986 Dihedral : 18.794 76.329 1060 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.51 % Allowed : 12.71 % 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: 1.45 (0.31), residues: 698 helix: 2.56 (0.26), residues: 346 sheet: -0.19 (0.61), residues: 61 loop : -0.79 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 766 TYR 0.007 0.001 TYR A 143 PHE 0.011 0.001 PHE A 8 TRP 0.010 0.001 TRP A 370 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6323) covalent geometry : angle 0.52950 / 0.28 ( 8724) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 0.35911 / 0.19 ( 2) hydrogen bonds : bond 0.04024 / 2.71 ( 355) hydrogen bonds : angle 3.98549 / 2.92 ( 985) metal coordination : bond 0.00080 / 0.04 ( 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 72 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.171 Fit side-chains REVERT: A 89 TRP cc_start: 0.7447 (p-90) cc_final: 0.7072 (p90) REVERT: A 167 GLU cc_start: 0.8026 (tt0) cc_final: 0.7737 (mt-10) REVERT: A 211 MET cc_start: 0.6422 (ttt) cc_final: 0.6095 (ttt) REVERT: A 214 GLN cc_start: 0.6476 (pp30) cc_final: 0.5920 (pp30) REVERT: A 372 LEU cc_start: 0.8420 (mp) cc_final: 0.8097 (mp) REVERT: A 593 LYS cc_start: 0.7821 (ptmt) cc_final: 0.7576 (ptmt) REVERT: A 642 ASP cc_start: 0.6532 (p0) cc_final: 0.6155 (p0) REVERT: A 652 ASP cc_start: 0.8502 (m-30) cc_final: 0.8098 (m-30) REVERT: A 720 ASP cc_start: 0.8093 (m-30) cc_final: 0.7758 (m-30) REVERT: A 763 ARG cc_start: 0.8190 (mmt-90) cc_final: 0.7703 (mmt90) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.0753 time to fit residues: 7.3878 Evaluate side-chains 68 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 697 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.0000 chunk 27 optimal weight: 0.0770 chunk 24 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 50.0000 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN A 664 GLN ** A 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.172313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.131975 restraints weight = 6139.385| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.66 r_work: 0.2938 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6326 Z= 0.112 Angle : 0.524 6.212 8726 Z= 0.275 Chirality : 0.040 0.139 1000 Planarity : 0.003 0.027 986 Dihedral : 18.797 76.562 1060 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.02 % Allowed : 12.37 % Favored : 86.61 % 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: 2.80 (0.26), residues: 340 sheet: -0.08 (0.61), residues: 61 loop : -0.70 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.007 0.001 TYR A 143 PHE 0.011 0.001 PHE A 8 TRP 0.009 0.001 TRP A 370 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6323) covalent geometry : angle 0.52440 / 0.28 ( 8724) SS BOND : bond 0.00135 / 0.07 ( 1) SS BOND : angle 0.25383 / 0.13 ( 2) hydrogen bonds : bond 0.03826 / 2.58 ( 355) hydrogen bonds : angle 3.89812 / 2.86 ( 985) metal coordination : bond 0.00152 / 0.08 ( 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 74 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.128 Fit side-chains REVERT: A 89 TRP cc_start: 0.7574 (p-90) cc_final: 0.7165 (p90) REVERT: A 167 GLU cc_start: 0.8105 (tt0) cc_final: 0.7808 (mt-10) REVERT: A 211 MET cc_start: 0.6438 (ttt) cc_final: 0.6111 (ttt) REVERT: A 214 GLN cc_start: 0.6607 (pp30) cc_final: 0.6041 (pp30) REVERT: A 372 LEU cc_start: 0.8497 (mp) cc_final: 0.8167 (mp) REVERT: A 593 LYS cc_start: 0.7922 (ptmt) cc_final: 0.7519 (ptmt) REVERT: A 642 ASP cc_start: 0.6634 (p0) cc_final: 0.6250 (p0) REVERT: A 720 ASP cc_start: 0.8108 (m-30) cc_final: 0.7785 (m-30) REVERT: A 763 ARG cc_start: 0.8243 (mmt-90) cc_final: 0.7773 (mmt90) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.0690 time to fit residues: 6.7930 Evaluate side-chains 69 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 771 ILE 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: 0.9980 chunk 67 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.171824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.142461 restraints weight = 5999.023| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.86 r_work: 0.3022 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2498 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= 0.119 Angle : 0.522 6.454 8726 Z= 0.273 Chirality : 0.040 0.140 1000 Planarity : 0.003 0.027 986 Dihedral : 18.866 77.275 1060 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.19 % Allowed : 13.39 % 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: 1.59 (0.31), residues: 698 helix: 2.73 (0.27), residues: 346 sheet: -0.05 (0.61), residues: 61 loop : -0.82 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.003 0.000 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6323) covalent geometry : angle 0.52169 / 0.27 ( 8724) SS BOND : bond 0.00142 / 0.07 ( 1) SS BOND : angle 0.10151 / 0.05 ( 2) hydrogen bonds : bond 0.03789 / 2.55 ( 355) hydrogen bonds : angle 3.86124 / 2.83 ( 985) metal coordination : bond 0.00179 / 0.09 ( 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 74 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.198 Fit side-chains REVERT: A 89 TRP cc_start: 0.7573 (p-90) cc_final: 0.7207 (p90) REVERT: A 167 GLU cc_start: 0.8007 (tt0) cc_final: 0.7770 (mt-10) REVERT: A 211 MET cc_start: 0.6831 (ttt) cc_final: 0.6550 (ttt) REVERT: A 214 GLN cc_start: 0.6587 (pp30) cc_final: 0.6060 (pp30) REVERT: A 372 LEU cc_start: 0.8505 (mp) cc_final: 0.8190 (mp) REVERT: A 593 LYS cc_start: 0.7884 (ptmt) cc_final: 0.7517 (ptmt) REVERT: A 642 ASP cc_start: 0.6538 (p0) cc_final: 0.6117 (p0) REVERT: A 720 ASP cc_start: 0.7932 (m-30) cc_final: 0.7636 (m-30) REVERT: A 763 ARG cc_start: 0.8172 (mmt-90) cc_final: 0.7692 (mmt90) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.0660 time to fit residues: 6.4616 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 : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.170832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.137818 restraints weight = 6047.702| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 0.94 r_work: 0.2970 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2599 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= 0.135 Angle : 0.544 7.442 8726 Z= 0.281 Chirality : 0.040 0.137 1000 Planarity : 0.003 0.027 986 Dihedral : 19.049 78.054 1060 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.36 % Allowed : 13.22 % 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: 1.59 (0.31), residues: 698 helix: 2.82 (0.27), residues: 344 sheet: -0.10 (0.60), residues: 61 loop : -0.91 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.008 0.001 TYR A 143 PHE 0.020 0.001 PHE A 378 TRP 0.009 0.001 TRP A 370 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 6323) covalent geometry : angle 0.54435 / 0.28 ( 8724) SS BOND : bond 0.00115 / 0.06 ( 1) SS BOND : angle 0.12583 / 0.07 ( 2) hydrogen bonds : bond 0.03890 / 2.61 ( 355) hydrogen bonds : angle 3.87091 / 2.85 ( 985) metal coordination : bond 0.00250 / 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 77 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.185 Fit side-chains REVERT: A 76 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8100 (ttp80) REVERT: A 89 TRP cc_start: 0.7533 (p-90) cc_final: 0.7153 (p90) REVERT: A 167 GLU cc_start: 0.7972 (tt0) cc_final: 0.7739 (mt-10) REVERT: A 211 MET cc_start: 0.7050 (ttt) cc_final: 0.6668 (ttt) REVERT: A 214 GLN cc_start: 0.6630 (pp30) cc_final: 0.6059 (pp30) REVERT: A 593 LYS cc_start: 0.7975 (ptmt) cc_final: 0.7626 (ptmt) REVERT: A 678 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8295 (mm) REVERT: A 720 ASP cc_start: 0.7937 (m-30) cc_final: 0.7658 (m-30) REVERT: A 763 ARG cc_start: 0.8232 (mmt-90) cc_final: 0.7739 (mmt90) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.0649 time to fit residues: 6.3923 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 : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 336 LEU 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 Chi-restraints excluded: chain A residue 771 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: 1.9990 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 41 optimal weight: 0.0570 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.170286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.130491 restraints weight = 6078.213| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.31 r_work: 0.2937 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2680 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= 0.140 Angle : 0.540 7.769 8726 Z= 0.282 Chirality : 0.040 0.136 1000 Planarity : 0.003 0.027 986 Dihedral : 19.108 79.018 1060 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.36 % Allowed : 13.56 % 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: 1.62 (0.31), residues: 698 helix: 2.87 (0.27), residues: 340 sheet: -0.16 (0.61), residues: 61 loop : -0.86 (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 0.013 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 0.00324 / 0.14 ( 6323) covalent geometry : angle 0.54018 / 0.28 ( 8724) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.18068 / 0.10 ( 2) hydrogen bonds : bond 0.03872 / 2.60 ( 355) hydrogen bonds : angle 3.86460 / 2.83 ( 985) metal coordination : bond 0.00237 / 0.12 ( 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 77 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.194 Fit side-chains REVERT: A 76 ARG cc_start: 0.8505 (ttm170) cc_final: 0.8193 (ttp80) REVERT: A 89 TRP cc_start: 0.7540 (p-90) cc_final: 0.7148 (p90) REVERT: A 167 GLU cc_start: 0.8065 (tt0) cc_final: 0.7806 (mt-10) REVERT: A 214 GLN cc_start: 0.6529 (pp30) cc_final: 0.5959 (pp30) REVERT: A 593 LYS cc_start: 0.8006 (ptmt) cc_final: 0.7659 (ptmt) REVERT: A 671 ILE cc_start: 0.8886 (tt) cc_final: 0.8456 (tp) REVERT: A 678 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8325 (mm) REVERT: A 720 ASP cc_start: 0.7974 (m-30) cc_final: 0.7717 (m-30) REVERT: A 763 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.7799 (mmt90) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.0519 time to fit residues: 5.3922 Evaluate side-chains 73 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 336 LEU 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 678 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.131030 restraints weight = 6090.923| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.19 r_work: 0.2927 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2765 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= 0.146 Angle : 0.544 7.831 8726 Z= 0.282 Chirality : 0.040 0.136 1000 Planarity : 0.004 0.027 986 Dihedral : 19.106 79.605 1060 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.19 % Allowed : 13.90 % Favored : 84.92 % 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: 1.50 (0.31), residues: 698 helix: 2.71 (0.27), residues: 346 sheet: -0.21 (0.61), residues: 61 loop : -0.93 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.008 0.001 TYR A 143 PHE 0.013 0.001 PHE A 8 TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6323) covalent geometry : angle 0.54454 / 0.28 ( 8724) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.18686 / 0.10 ( 2) hydrogen bonds : bond 0.03909 / 2.63 ( 355) hydrogen bonds : angle 3.88728 / 2.85 ( 985) metal coordination : bond 0.00261 / 0.13 ( 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 76 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.210 Fit side-chains REVERT: A 76 ARG cc_start: 0.8494 (ttm170) cc_final: 0.8163 (ttp80) REVERT: A 89 TRP cc_start: 0.7490 (p-90) cc_final: 0.7079 (p90) REVERT: A 167 GLU cc_start: 0.8042 (tt0) cc_final: 0.7740 (mt-10) REVERT: A 214 GLN cc_start: 0.6555 (pp30) cc_final: 0.5991 (pp30) REVERT: A 593 LYS cc_start: 0.7978 (ptmt) cc_final: 0.7665 (ptmt) REVERT: A 678 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 720 ASP cc_start: 0.7905 (m-30) cc_final: 0.7679 (m-30) REVERT: A 763 ARG cc_start: 0.8270 (mmt-90) cc_final: 0.7766 (mmt90) outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.0650 time to fit residues: 6.6309 Evaluate side-chains 72 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 LEU 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 678 ILE Chi-restraints excluded: chain A residue 771 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.169413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.132975 restraints weight = 6061.814| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.06 r_work: 0.2943 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6326 Z= 0.156 Angle : 0.556 8.502 8726 Z= 0.287 Chirality : 0.040 0.140 1000 Planarity : 0.004 0.028 986 Dihedral : 18.935 80.357 1060 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.36 % Allowed : 14.07 % 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: 1.48 (0.31), residues: 698 helix: 2.74 (0.27), residues: 340 sheet: -0.45 (0.59), residues: 63 loop : -0.85 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.009 0.001 TYR A 143 PHE 0.013 0.001 PHE A 8 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 6323) covalent geometry : angle 0.55570 / 0.29 ( 8724) SS BOND : bond 0.00046 / 0.02 ( 1) SS BOND : angle 0.21359 / 0.11 ( 2) hydrogen bonds : bond 0.03977 / 2.67 ( 355) hydrogen bonds : angle 3.89393 / 2.85 ( 985) metal coordination : bond 0.00314 / 0.16 ( 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 79 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.175 Fit side-chains REVERT: A 76 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8165 (ttp80) REVERT: A 89 TRP cc_start: 0.7467 (p-90) cc_final: 0.7087 (p90) REVERT: A 167 GLU cc_start: 0.8062 (tt0) cc_final: 0.7774 (mt-10) REVERT: A 214 GLN cc_start: 0.6612 (pp30) cc_final: 0.6062 (pp30) REVERT: A 593 LYS cc_start: 0.8002 (ptmt) cc_final: 0.7676 (ptmt) REVERT: A 671 ILE cc_start: 0.8898 (tt) cc_final: 0.8519 (tp) REVERT: A 678 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8578 (mm) REVERT: A 720 ASP cc_start: 0.7862 (m-30) cc_final: 0.7636 (m-30) REVERT: A 763 ARG cc_start: 0.8287 (mmt-90) cc_final: 0.7808 (mmt90) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.0677 time to fit residues: 6.9905 Evaluate side-chains 74 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 LEU 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 Chi-restraints excluded: chain A residue 771 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.165164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.117264 restraints weight = 6110.631| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.53 r_work: 0.2894 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2936 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= 0.122 Angle : 0.524 8.249 8726 Z= 0.272 Chirality : 0.039 0.137 1000 Planarity : 0.003 0.029 986 Dihedral : 18.892 81.239 1060 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.68 % Allowed : 14.58 % Favored : 84.75 % 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: 1.53 (0.31), residues: 698 helix: 2.73 (0.27), residues: 346 sheet: -0.37 (0.60), residues: 63 loop : -0.86 (0.34), residues: 289 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 0.011 0.001 PHE A 8 TRP 0.010 0.001 TRP A 370 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6323) covalent geometry : angle 0.52372 / 0.27 ( 8724) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 0.30702 / 0.16 ( 2) hydrogen bonds : bond 0.03690 / 2.48 ( 355) hydrogen bonds : angle 3.83779 / 2.82 ( 985) metal coordination : bond 0.00157 / 0.08 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.02 seconds wall clock time: 28 minutes 14.01 seconds (1694.01 seconds total)