Starting phenix.real_space_refine on Thu Jul 2 08:23:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lcx_62995/07_2026/9lcx_62995.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lcx_62995/07_2026/9lcx_62995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lcx_62995/07_2026/9lcx_62995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lcx_62995/07_2026/9lcx_62995.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lcx_62995/07_2026/9lcx_62995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lcx_62995/07_2026/9lcx_62995.map" } resolution = 3.18 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= 0.001 sd= 0.160 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 186 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 58 5.49 5 S 21 5.16 5 C 4506 2.51 5 N 1362 2.21 5 O 1538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s 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: 7486 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6296 Classifications: {'peptide': 854} Link IDs: {'PTRANS': 47, 'TRANS': 806} Chain: "C" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 599 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "B" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 590 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5985 SG CYS A 842 33.481 53.845 30.045 1.00 57.04 S ATOM 6007 SG CYS A 845 36.075 53.091 26.348 1.00 57.53 S Time building chain proxies: 1.33, per 1000 atoms: 0.18 Number of scatterers: 7486 At special positions: 0 Unit cell: (82.9521, 82.9521, 131.431, 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 21 16.00 P 58 15.00 O 1538 8.00 N 1362 7.00 C 4506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 237.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 814 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 845 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 842 " 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 1 sheets defined 71.7% alpha, 3.3% beta 11 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 33 through 48 removed outlier: 4.281A pdb=" N SER A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N THR A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 63 through 81 removed outlier: 4.073A pdb=" N LEU A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.679A pdb=" N THR A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.532A pdb=" N ARG A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 166 through 184 removed outlier: 3.684A pdb=" N ALA A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.958A pdb=" N ARG A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 234 through 250 removed outlier: 3.879A pdb=" N ARG A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 268 through 284 removed outlier: 3.606A pdb=" N ALA A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 302 through 320 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 336 through 352 removed outlier: 3.679A pdb=" N ALA A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 370 through 389 Proline residue: A 383 - end of helix removed outlier: 4.034A pdb=" N GLN A 387 " --> pdb=" O PRO A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 404 through 423 Proline residue: A 417 - end of helix removed outlier: 4.242A pdb=" N GLN A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 439 through 454 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 472 through 488 removed outlier: 3.536A pdb=" N ALA A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.549A pdb=" N ALA A 510 " --> pdb=" O GLY A 506 " (cutoff:3.500A) Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 540 through 556 Proline residue: A 553 - end of helix removed outlier: 3.683A pdb=" N CYS A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 574 through 593 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 608 through 626 Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 644 through 661 removed outlier: 3.709A pdb=" N VAL A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 664 through 673 Processing helix chain 'A' and resid 676 through 691 removed outlier: 3.836A pdb=" N ALA A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 702 Processing helix chain 'A' and resid 715 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.785A pdb=" N THR A 807 " --> pdb=" O PRO A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 826 Processing helix chain 'A' and resid 843 through 852 removed outlier: 3.998A pdb=" N THR A 847 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET A 848 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR A 849 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 768 removed outlier: 4.633A pdb=" N ALA A 708 " --> pdb=" O GLY A 796 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1779 1.33 - 1.45: 1588 1.45 - 1.57: 4222 1.57 - 1.69: 114 1.69 - 1.81: 25 Bond restraints: 7728 Sorted by residual: bond pdb=" C3' DG B -24 " pdb=" C2' DG B -24 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.82e+00 bond pdb=" C3' DG C 10 " pdb=" C2' DG C 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.71e+00 bond pdb=" C3' DT C -4 " pdb=" C2' DT C -4 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.46e+00 bond pdb=" C3' DA C 23 " pdb=" C2' DA C 23 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.19e+00 bond pdb=" C3' DA B -8 " pdb=" C2' DA B -8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.19e+00 ... (remaining 7723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 10085 1.20 - 2.41: 572 2.41 - 3.61: 96 3.61 - 4.81: 20 4.81 - 6.01: 5 Bond angle restraints: 10778 Sorted by residual: angle pdb=" N3 DT B -7 " pdb=" C4 DT B -7 " pdb=" O4 DT B -7 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT B -14 " pdb=" C4 DT B -14 " pdb=" O4 DT B -14 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT B 1 " pdb=" C4 DT B 1 " pdb=" O4 DT B 1 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 16 " pdb=" C4 DT C 16 " pdb=" O4 DT C 16 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 10773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 4214 34.82 - 69.65: 291 69.65 - 104.47: 7 104.47 - 139.29: 1 139.29 - 174.12: 2 Dihedral angle restraints: 4515 sinusoidal: 2104 harmonic: 2411 Sorted by residual: dihedral pdb=" C4' DG C 2 " pdb=" C3' DG C 2 " pdb=" O3' DG C 2 " pdb=" P DG C 3 " ideal model delta sinusoidal sigma weight residual 220.00 45.88 174.12 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT C -4 " pdb=" C3' DT C -4 " pdb=" O3' DT C -4 " pdb=" P DC C -3 " ideal model delta sinusoidal sigma weight residual 220.00 75.30 144.70 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DC C 1 " pdb=" C3' DC C 1 " pdb=" O3' DC C 1 " pdb=" P DG C 2 " ideal model delta sinusoidal sigma weight residual 220.00 83.75 136.25 1 3.50e+01 8.16e-04 1.35e+01 ... (remaining 4512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 701 0.029 - 0.057: 335 0.057 - 0.086: 157 0.086 - 0.114: 101 0.114 - 0.143: 5 Chirality restraints: 1299 Sorted by residual: chirality pdb=" C3' DG C 2 " pdb=" C4' DG C 2 " pdb=" O3' DG C 2 " pdb=" C2' DG C 2 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE A 795 " pdb=" N ILE A 795 " pdb=" C ILE A 795 " pdb=" CB ILE A 795 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" C3' DT C -4 " pdb=" C4' DT C -4 " pdb=" O3' DT C -4 " pdb=" C2' DT C -4 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 1296 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 427 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 552 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO A 553 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 290 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 291 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.025 5.00e-02 4.00e+02 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1510 2.79 - 3.32: 6801 3.32 - 3.84: 12058 3.84 - 4.37: 15293 4.37 - 4.90: 25254 Nonbonded interactions: 60916 Sorted by model distance: nonbonded pdb=" O VAL A 329 " pdb=" OG SER A 333 " model vdw 2.260 3.040 nonbonded pdb=" O VAL A 431 " pdb=" OG SER A 435 " model vdw 2.272 3.040 nonbonded pdb=" O HIS A 140 " pdb=" NH1 ARG A 143 " model vdw 2.276 3.120 nonbonded pdb=" O VAL A 261 " pdb=" OG SER A 265 " model vdw 2.279 3.040 nonbonded pdb=" NH2 ARG A 100 " pdb=" OP2 DG B -24 " model vdw 2.293 3.120 ... (remaining 60911 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.370 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.006 0.214 7731 Z= 0.374 Angle : 0.642 6.015 10778 Z= 0.459 Chirality : 0.044 0.143 1299 Planarity : 0.006 0.053 1206 Dihedral : 19.351 174.117 2967 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.28), residues: 852 helix: -0.57 (0.20), residues: 595 sheet: -0.94 (0.68), residues: 52 loop : -0.91 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 810 TYR 0.017 0.001 TYR A 697 PHE 0.009 0.001 PHE A 797 TRP 0.005 0.001 TRP A 773 HIS 0.012 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.36 ( 7728) covalent geometry : angle 0.64158 / 0.46 (10778) hydrogen bonds : bond 0.15821 / 11.54 ( 408) hydrogen bonds : angle 6.80362 / 4.77 ( 1171) metal coordination : bond 0.12374 / 6.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.191 Fit side-chains REVERT: A 724 ASN cc_start: 0.8113 (t0) cc_final: 0.7113 (t0) REVERT: A 728 ASN cc_start: 0.7995 (m110) cc_final: 0.7464 (m-40) REVERT: A 775 LEU cc_start: 0.8558 (mp) cc_final: 0.8306 (mp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0498 time to fit residues: 3.8602 Evaluate side-chains 41 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 HIS ** A 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.193366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.161507 restraints weight = 7373.499| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.03 r_work: 0.3310 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7731 Z= 0.141 Angle : 0.606 7.039 10778 Z= 0.334 Chirality : 0.044 0.289 1299 Planarity : 0.005 0.050 1206 Dihedral : 21.786 174.960 1520 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.30 % Allowed : 4.45 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.29), residues: 852 helix: -0.07 (0.21), residues: 604 sheet: -0.91 (0.67), residues: 54 loop : -0.88 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.017 0.002 TYR A 697 PHE 0.006 0.001 PHE A 797 TRP 0.004 0.001 TRP A 773 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 7728) covalent geometry : angle 0.60618 / 0.33 (10778) hydrogen bonds : bond 0.04244 / 3.01 ( 408) hydrogen bonds : angle 4.64793 / 3.30 ( 1171) metal coordination : bond 0.01079 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.210 Fit side-chains REVERT: A 125 LEU cc_start: 0.7808 (mt) cc_final: 0.7438 (mt) REVERT: A 625 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7375 (mm-40) REVERT: A 724 ASN cc_start: 0.7953 (t0) cc_final: 0.7588 (t0) REVERT: A 775 LEU cc_start: 0.8645 (mp) cc_final: 0.8365 (mp) REVERT: A 844 TYR cc_start: 0.8349 (m-80) cc_final: 0.8112 (m-80) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.0446 time to fit residues: 3.7870 Evaluate side-chains 46 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 HIS A 836 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.189671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149836 restraints weight = 7263.172| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.39 r_work: 0.3238 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7731 Z= 0.140 Angle : 0.562 7.160 10778 Z= 0.310 Chirality : 0.042 0.290 1299 Planarity : 0.005 0.048 1206 Dihedral : 22.243 172.197 1520 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.59 % Allowed : 6.38 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.29), residues: 852 helix: 0.22 (0.21), residues: 605 sheet: -0.64 (0.70), residues: 54 loop : -0.64 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.017 0.001 TYR A 697 PHE 0.006 0.001 PHE A 797 TRP 0.004 0.001 TRP A 96 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 7728) covalent geometry : angle 0.56234 / 0.31 (10778) hydrogen bonds : bond 0.03531 / 2.46 ( 408) hydrogen bonds : angle 4.38153 / 3.13 ( 1171) metal coordination : bond 0.00623 / 0.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.143 Fit side-chains REVERT: A 125 LEU cc_start: 0.7515 (mt) cc_final: 0.7105 (mt) REVERT: A 216 CYS cc_start: 0.7761 (m) cc_final: 0.7349 (t) REVERT: A 724 ASN cc_start: 0.7933 (t0) cc_final: 0.7541 (t0) outliers start: 4 outliers final: 1 residues processed: 53 average time/residue: 0.0444 time to fit residues: 3.8686 Evaluate side-chains 50 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 79 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 836 ASN ** 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 = 0.4098 r_free = 0.4098 target = 0.192446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.157545 restraints weight = 7469.355| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.20 r_work: 0.3255 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7731 Z= 0.150 Angle : 0.571 6.976 10778 Z= 0.310 Chirality : 0.043 0.283 1299 Planarity : 0.004 0.048 1206 Dihedral : 22.413 174.015 1520 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.45 % Allowed : 8.01 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.29), residues: 852 helix: 0.28 (0.21), residues: 606 sheet: -0.51 (0.69), residues: 54 loop : -0.53 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.016 0.001 TYR A 697 PHE 0.007 0.001 PHE A 797 TRP 0.003 0.001 TRP A 96 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 7728) covalent geometry : angle 0.57100 / 0.31 (10778) hydrogen bonds : bond 0.03376 / 2.35 ( 408) hydrogen bonds : angle 4.31315 / 3.09 ( 1171) metal coordination : bond 0.00088 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.188 Fit side-chains REVERT: A 125 LEU cc_start: 0.7613 (mt) cc_final: 0.7192 (mt) REVERT: A 216 CYS cc_start: 0.7725 (m) cc_final: 0.7334 (t) REVERT: A 625 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7264 (mm-40) REVERT: A 724 ASN cc_start: 0.7941 (t0) cc_final: 0.7580 (t0) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.0459 time to fit residues: 4.0632 Evaluate side-chains 51 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 836 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.190843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150981 restraints weight = 7315.969| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.39 r_work: 0.3278 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7731 Z= 0.122 Angle : 0.536 6.461 10778 Z= 0.292 Chirality : 0.041 0.271 1299 Planarity : 0.004 0.047 1206 Dihedral : 22.421 176.625 1520 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.59 % Allowed : 10.24 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.29), residues: 852 helix: 0.49 (0.21), residues: 605 sheet: -0.48 (0.71), residues: 54 loop : -0.41 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 710 TYR 0.016 0.001 TYR A 697 PHE 0.004 0.001 PHE A 797 TRP 0.002 0.000 TRP A 96 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 7728) covalent geometry : angle 0.53590 / 0.29 (10778) hydrogen bonds : bond 0.02965 / 2.04 ( 408) hydrogen bonds : angle 4.18126 / 3.00 ( 1171) metal coordination : bond 0.00248 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.153 Fit side-chains REVERT: A 125 LEU cc_start: 0.7544 (mt) cc_final: 0.7111 (mt) REVERT: A 216 CYS cc_start: 0.7663 (m) cc_final: 0.7294 (t) REVERT: A 724 ASN cc_start: 0.7970 (t0) cc_final: 0.7650 (t0) outliers start: 4 outliers final: 1 residues processed: 57 average time/residue: 0.0543 time to fit residues: 5.0379 Evaluate side-chains 54 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 52 optimal weight: 0.0020 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 835 HIS A 836 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.193958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.155610 restraints weight = 7364.186| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.34 r_work: 0.3244 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7731 Z= 0.129 Angle : 0.533 6.272 10778 Z= 0.290 Chirality : 0.041 0.267 1299 Planarity : 0.004 0.046 1206 Dihedral : 22.437 178.174 1520 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.89 % Allowed : 10.98 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.29), residues: 852 helix: 0.53 (0.21), residues: 605 sheet: -0.57 (0.71), residues: 56 loop : -0.70 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 710 TYR 0.015 0.001 TYR A 697 PHE 0.005 0.001 PHE A 797 TRP 0.002 0.000 TRP A 96 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 7728) covalent geometry : angle 0.53333 / 0.29 (10778) hydrogen bonds : bond 0.02962 / 2.04 ( 408) hydrogen bonds : angle 4.14010 / 2.97 ( 1171) metal coordination : bond 0.00156 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.254 Fit side-chains REVERT: A 125 LEU cc_start: 0.7582 (mt) cc_final: 0.7120 (mt) REVERT: A 216 CYS cc_start: 0.7643 (m) cc_final: 0.7269 (t) REVERT: A 724 ASN cc_start: 0.7924 (t0) cc_final: 0.7715 (t0) REVERT: A 844 TYR cc_start: 0.8608 (m-80) cc_final: 0.8203 (m-80) outliers start: 6 outliers final: 4 residues processed: 59 average time/residue: 0.0526 time to fit residues: 5.1713 Evaluate side-chains 55 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 56 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 835 HIS A 836 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.191655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151538 restraints weight = 7408.563| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.41 r_work: 0.3235 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7731 Z= 0.169 Angle : 0.573 6.279 10778 Z= 0.309 Chirality : 0.043 0.272 1299 Planarity : 0.004 0.047 1206 Dihedral : 22.580 179.100 1520 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.04 % Allowed : 11.42 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.29), residues: 852 helix: 0.41 (0.21), residues: 606 sheet: -0.67 (0.70), residues: 56 loop : -0.69 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 244 TYR 0.015 0.001 TYR A 697 PHE 0.007 0.001 PHE A 797 TRP 0.002 0.001 TRP A 96 HIS 0.005 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 7728) covalent geometry : angle 0.57284 / 0.31 (10778) hydrogen bonds : bond 0.03387 / 2.36 ( 408) hydrogen bonds : angle 4.22309 / 3.03 ( 1171) metal coordination : bond 0.00279 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.268 Fit side-chains REVERT: A 216 CYS cc_start: 0.7695 (m) cc_final: 0.7303 (t) REVERT: A 779 ASP cc_start: 0.7549 (p0) cc_final: 0.6963 (p0) REVERT: A 844 TYR cc_start: 0.8749 (m-80) cc_final: 0.8362 (m-10) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.0524 time to fit residues: 5.0588 Evaluate side-chains 56 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 835 HIS A 836 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.192910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152653 restraints weight = 7438.733| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.41 r_work: 0.3237 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7731 Z= 0.142 Angle : 0.555 6.802 10778 Z= 0.299 Chirality : 0.042 0.268 1299 Planarity : 0.004 0.047 1206 Dihedral : 22.529 179.015 1520 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.19 % Allowed : 11.42 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.29), residues: 852 helix: 0.47 (0.21), residues: 606 sheet: -0.65 (0.70), residues: 56 loop : -0.69 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 244 TYR 0.016 0.001 TYR A 697 PHE 0.006 0.001 PHE A 797 TRP 0.003 0.001 TRP A 96 HIS 0.006 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 7728) covalent geometry : angle 0.55466 / 0.30 (10778) hydrogen bonds : bond 0.03136 / 2.18 ( 408) hydrogen bonds : angle 4.19149 / 3.01 ( 1171) metal coordination : bond 0.00190 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.299 Fit side-chains REVERT: A 125 LEU cc_start: 0.7583 (mt) cc_final: 0.7199 (mt) REVERT: A 216 CYS cc_start: 0.7741 (m) cc_final: 0.7365 (t) REVERT: A 779 ASP cc_start: 0.7610 (p0) cc_final: 0.7012 (p0) REVERT: A 844 TYR cc_start: 0.8693 (m-80) cc_final: 0.8420 (m-80) outliers start: 8 outliers final: 7 residues processed: 59 average time/residue: 0.0554 time to fit residues: 5.3821 Evaluate side-chains 59 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 841 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 835 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.189598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.150048 restraints weight = 7316.816| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.47 r_work: 0.3243 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7731 Z= 0.137 Angle : 0.549 6.773 10778 Z= 0.297 Chirality : 0.041 0.267 1299 Planarity : 0.004 0.046 1206 Dihedral : 22.504 179.136 1520 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.04 % Allowed : 12.02 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.29), residues: 852 helix: 0.50 (0.21), residues: 606 sheet: -0.64 (0.70), residues: 56 loop : -0.69 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 244 TYR 0.016 0.001 TYR A 697 PHE 0.006 0.001 PHE A 797 TRP 0.003 0.000 TRP A 96 HIS 0.008 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 7728) covalent geometry : angle 0.54897 / 0.30 (10778) hydrogen bonds : bond 0.03082 / 2.14 ( 408) hydrogen bonds : angle 4.16894 / 3.00 ( 1171) metal coordination : bond 0.00181 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.188 Fit side-chains REVERT: A 125 LEU cc_start: 0.7556 (mt) cc_final: 0.7164 (mt) REVERT: A 216 CYS cc_start: 0.7734 (m) cc_final: 0.7381 (t) REVERT: A 625 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7263 (mm-40) REVERT: A 779 ASP cc_start: 0.7604 (p0) cc_final: 0.7017 (p0) REVERT: A 844 TYR cc_start: 0.8704 (m-80) cc_final: 0.8443 (m-80) outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.0567 time to fit residues: 5.3413 Evaluate side-chains 57 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 841 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.0970 chunk 79 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN A 836 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.191500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151105 restraints weight = 7401.779| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.39 r_work: 0.3252 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7731 Z= 0.126 Angle : 0.531 6.786 10778 Z= 0.289 Chirality : 0.041 0.265 1299 Planarity : 0.004 0.046 1206 Dihedral : 22.375 179.191 1520 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.19 % Allowed : 12.17 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.29), residues: 852 helix: 0.58 (0.21), residues: 605 sheet: -0.60 (0.70), residues: 56 loop : -0.66 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 244 TYR 0.016 0.001 TYR A 697 PHE 0.005 0.001 PHE A 797 TRP 0.002 0.000 TRP A 96 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 7728) covalent geometry : angle 0.53097 / 0.29 (10778) hydrogen bonds : bond 0.02881 / 2.00 ( 408) hydrogen bonds : angle 4.09343 / 2.94 ( 1171) metal coordination : bond 0.00161 / 0.08 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.242 Fit side-chains REVERT: A 125 LEU cc_start: 0.7526 (mt) cc_final: 0.7131 (mt) REVERT: A 216 CYS cc_start: 0.7649 (m) cc_final: 0.7332 (t) REVERT: A 339 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8632 (mm110) REVERT: A 625 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7287 (mm-40) REVERT: A 728 ASN cc_start: 0.8451 (m110) cc_final: 0.7876 (m110) REVERT: A 844 TYR cc_start: 0.8622 (m-80) cc_final: 0.8410 (m-80) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.0492 time to fit residues: 4.9414 Evaluate side-chains 59 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 836 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.194568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152948 restraints weight = 7436.359| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.51 r_work: 0.3239 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.412 7731 Z= 0.444 Angle : 1.147 59.194 10778 Z= 0.736 Chirality : 0.051 1.087 1299 Planarity : 0.005 0.109 1206 Dihedral : 22.372 179.197 1520 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.89 % Allowed : 12.61 % Favored : 86.50 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.29), residues: 852 helix: 0.56 (0.21), residues: 605 sheet: -0.45 (0.68), residues: 56 loop : -0.66 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 244 TYR 0.016 0.001 TYR A 697 PHE 0.005 0.001 PHE A 797 TRP 0.003 0.001 TRP A 96 HIS 0.003 0.000 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00873 / 0.44 ( 7728) covalent geometry : angle 1.14718 / 0.74 (10778) hydrogen bonds : bond 0.02932 / 2.04 ( 408) hydrogen bonds : angle 4.09327 / 2.94 ( 1171) metal coordination : bond 0.00175 / 0.09 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1346.63 seconds wall clock time: 23 minutes 45.23 seconds (1425.23 seconds total)