Starting phenix.real_space_refine on Wed Aug 5 00:48:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lcx_62995/08_2026/9lcx_62995.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lcx_62995/08_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_62995/08_2026/9lcx_62995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lcx_62995/08_2026/9lcx_62995.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lcx_62995/08_2026/9lcx_62995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lcx_62995/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.76, per 1000 atoms: 0.24 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: 0.72 Conformation dependent library (CDL) restraints added in 343.9 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: 0.92 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: 1.30 Time building geometry restraints manager: 0.94 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: 10078 1.20 - 2.41: 578 2.41 - 3.61: 96 3.61 - 4.81: 21 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.000 Find NCS groups from input model: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.680 ------------------------------------------------------------------------------- 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 : 0.644 6.015 10778 Z= 0.462 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 0.64436 / 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 : 0.229 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: 0.0639 time to fit residues: 4.9676 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 : 0.252 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.193538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.161186 restraints weight = 7370.233| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.00 r_work: 0.3336 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7731 Z= 0.142 Angle : 0.611 7.507 10778 Z= 0.338 Chirality : 0.044 0.290 1299 Planarity : 0.005 0.049 1206 Dihedral : 21.795 175.606 1520 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.30 % Allowed : 4.30 % Favored : 95.40 % 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: -0.60 (0.29), residues: 852 helix: -0.05 (0.21), residues: 604 sheet: -0.90 (0.68), residues: 54 loop : -0.88 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 810 TYR 0.017 0.002 TYR A 697 PHE 0.006 0.001 PHE A 797 TRP 0.003 0.001 TRP A 773 HIS 0.005 0.001 HIS A 814 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 ( 7728) covalent geometry : angle 0.61070 / 0.34 (10778) hydrogen bonds : bond 0.04006 / 2.83 ( 408) hydrogen bonds : angle 4.60372 / 3.27 ( 1171) metal coordination : bond 0.01962 / 1.03 ( 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 : 0.239 Fit side-chains REVERT: A 125 LEU cc_start: 0.7779 (mt) cc_final: 0.7411 (mt) REVERT: A 625 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7343 (mm-40) REVERT: A 724 ASN cc_start: 0.7967 (t0) cc_final: 0.7587 (t0) REVERT: A 775 LEU cc_start: 0.8634 (mp) cc_final: 0.8333 (mp) REVERT: A 844 TYR cc_start: 0.8342 (m-80) cc_final: 0.8132 (m-80) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.0520 time to fit residues: 4.4806 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 : 0.231 ------------------------------------------------------------------------------- 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: 0.7980 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 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 = 0.4101 r_free = 0.4101 target = 0.192838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.152345 restraints weight = 7321.779| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.44 r_work: 0.3240 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1016 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= 0.145 Angle : 0.574 7.419 10778 Z= 0.313 Chirality : 0.043 0.309 1299 Planarity : 0.005 0.048 1206 Dihedral : 22.258 174.478 1520 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.45 % Allowed : 6.53 % 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: -0.21 (0.29), residues: 852 helix: 0.20 (0.21), residues: 605 sheet: -0.65 (0.69), 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 0.016 0.001 TYR A 697 PHE 0.007 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 0.00302 / 0.14 ( 7728) covalent geometry : angle 0.57437 / 0.31 (10778) hydrogen bonds : bond 0.03608 / 2.52 ( 408) hydrogen bonds : angle 4.38828 / 3.14 ( 1171) metal coordination : bond 0.00665 / 0.35 ( 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 52 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.237 Fit side-chains REVERT: A 125 LEU cc_start: 0.7506 (mt) cc_final: 0.7096 (mt) REVERT: A 216 CYS cc_start: 0.7754 (m) cc_final: 0.7332 (t) REVERT: A 724 ASN cc_start: 0.7941 (t0) cc_final: 0.7560 (t0) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.0536 time to fit residues: 4.5599 Evaluate side-chains 49 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 63 optimal weight: 0.0570 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 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: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 836 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.192965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159743 restraints weight = 7478.512| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.21 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1153 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 : 0.568 7.065 10778 Z= 0.307 Chirality : 0.042 0.296 1299 Planarity : 0.004 0.047 1206 Dihedral : 22.378 177.133 1520 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.45 % Allowed : 8.31 % Favored : 91.25 % 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: 0.03 (0.29), residues: 852 helix: 0.35 (0.21), residues: 605 sheet: -0.34 (0.71), residues: 52 loop : -0.52 (0.47), residues: 195 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 0.006 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 0.00301 / 0.14 ( 7728) covalent geometry : angle 0.56759 / 0.31 (10778) hydrogen bonds : bond 0.03256 / 2.26 ( 408) hydrogen bonds : angle 4.27803 / 3.06 ( 1171) metal coordination : bond 0.00139 / 0.07 ( 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 54 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.244 Fit side-chains REVERT: A 125 LEU cc_start: 0.8064 (mt) cc_final: 0.7710 (mt) REVERT: A 724 ASN cc_start: 0.8071 (t0) cc_final: 0.7755 (t0) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.0538 time to fit residues: 4.8494 Evaluate side-chains 53 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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: 1.9990 chunk 6 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 185 HIS A 835 HIS 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 = 0.194007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.152635 restraints weight = 7398.112| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.49 r_work: 0.3238 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1282 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= 0.130 Angle : 0.548 6.723 10778 Z= 0.296 Chirality : 0.042 0.291 1299 Planarity : 0.004 0.047 1206 Dihedral : 22.430 179.276 1520 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.59 % Allowed : 10.83 % Favored : 88.58 % 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: 0.46 (0.21), residues: 605 sheet: -0.64 (0.69), residues: 56 loop : -0.53 (0.48), residues: 191 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 0.006 0.001 PHE A 797 TRP 0.003 0.000 TRP A 96 HIS 0.004 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 7728) covalent geometry : angle 0.54837 / 0.30 (10778) hydrogen bonds : bond 0.03061 / 2.11 ( 408) hydrogen bonds : angle 4.19621 / 3.01 ( 1171) metal coordination : bond 0.00210 / 0.11 ( 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 : 0.229 Fit side-chains REVERT: A 125 LEU cc_start: 0.7558 (mt) cc_final: 0.7118 (mt) REVERT: A 724 ASN cc_start: 0.7945 (t0) cc_final: 0.7698 (t0) REVERT: A 779 ASP cc_start: 0.7542 (p0) cc_final: 0.7177 (p0) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 0.0541 time to fit residues: 5.0896 Evaluate side-chains 55 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.191392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151553 restraints weight = 7315.664| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.37 r_work: 0.3253 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1319 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= 0.139 Angle : 0.553 6.564 10778 Z= 0.298 Chirality : 0.042 0.288 1299 Planarity : 0.004 0.047 1206 Dihedral : 22.459 179.774 1520 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.74 % Allowed : 11.13 % 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: 0.08 (0.29), residues: 852 helix: 0.45 (0.21), residues: 606 sheet: -0.59 (0.69), residues: 56 loop : -0.67 (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 0.006 0.001 PHE A 797 TRP 0.003 0.001 TRP A 142 HIS 0.005 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 7728) covalent geometry : angle 0.55253 / 0.30 (10778) hydrogen bonds : bond 0.03094 / 2.14 ( 408) hydrogen bonds : angle 4.18570 / 3.00 ( 1171) metal coordination : bond 0.00212 / 0.11 ( 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 57 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.239 Fit side-chains REVERT: A 625 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7274 (mm-40) REVERT: A 724 ASN cc_start: 0.7936 (t0) cc_final: 0.7727 (t0) REVERT: A 779 ASP cc_start: 0.7477 (p0) cc_final: 0.6829 (p0) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.0515 time to fit residues: 4.8135 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 : 0.229 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 56 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.189148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.149453 restraints weight = 7358.289| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.37 r_work: 0.3275 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1334 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= 0.151 Angle : 0.562 6.485 10778 Z= 0.302 Chirality : 0.042 0.290 1299 Planarity : 0.004 0.047 1206 Dihedral : 22.489 179.308 1520 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.89 % Allowed : 11.57 % 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: 0.05 (0.29), residues: 852 helix: 0.42 (0.21), residues: 607 sheet: -0.59 (0.69), residues: 56 loop : -0.64 (0.47), residues: 189 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 0.006 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 0.00337 / 0.15 ( 7728) covalent geometry : angle 0.56247 / 0.30 (10778) hydrogen bonds : bond 0.03217 / 2.23 ( 408) hydrogen bonds : angle 4.19133 / 3.01 ( 1171) metal coordination : bond 0.00222 / 0.12 ( 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: 6 poor density : 54 time to evaluate : 0.247 Fit side-chains REVERT: A 125 LEU cc_start: 0.7504 (mt) cc_final: 0.7120 (mt) REVERT: A 779 ASP cc_start: 0.7509 (p0) cc_final: 0.6842 (p0) REVERT: A 844 TYR cc_start: 0.8669 (m-80) cc_final: 0.8386 (m-80) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.0514 time to fit residues: 5.0738 Evaluate side-chains 57 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.192927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153056 restraints weight = 7446.561| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.39 r_work: 0.3278 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1381 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= 0.148 Angle : 0.563 6.895 10778 Z= 0.302 Chirality : 0.042 0.290 1299 Planarity : 0.004 0.047 1206 Dihedral : 22.474 179.293 1520 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: 0.06 (0.29), residues: 852 helix: 0.43 (0.21), residues: 607 sheet: -0.61 (0.69), residues: 56 loop : -0.65 (0.47), residues: 189 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 0.007 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 7728) covalent geometry : angle 0.56348 / 0.30 (10778) hydrogen bonds : bond 0.03189 / 2.22 ( 408) hydrogen bonds : angle 4.18816 / 3.01 ( 1171) metal coordination : bond 0.00202 / 0.11 ( 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 : 0.261 Fit side-chains REVERT: A 125 LEU cc_start: 0.7435 (mt) cc_final: 0.7025 (mt) REVERT: A 625 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7206 (mm-40) REVERT: A 779 ASP cc_start: 0.7479 (p0) cc_final: 0.6830 (p0) REVERT: A 844 TYR cc_start: 0.8733 (m-80) cc_final: 0.8453 (m-80) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.0540 time to fit residues: 5.3095 Evaluate side-chains 58 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 0.0470 chunk 35 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN A 835 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.194080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153671 restraints weight = 7404.279| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.31 r_work: 0.3300 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1458 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= 0.128 Angle : 0.542 6.749 10778 Z= 0.293 Chirality : 0.041 0.287 1299 Planarity : 0.004 0.046 1206 Dihedral : 22.370 179.367 1520 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.59 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: 0.18 (0.29), residues: 852 helix: 0.52 (0.21), residues: 606 sheet: -0.38 (0.71), residues: 54 loop : -0.68 (0.47), residues: 192 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 0.005 0.001 PHE A 797 TRP 0.003 0.000 TRP A 96 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 7728) covalent geometry : angle 0.54222 / 0.29 (10778) hydrogen bonds : bond 0.02957 / 2.05 ( 408) hydrogen bonds : angle 4.11844 / 2.96 ( 1171) metal coordination : bond 0.00176 / 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 60 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.147 Fit side-chains REVERT: A 125 LEU cc_start: 0.7448 (mt) cc_final: 0.7040 (mt) REVERT: A 339 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8612 (mm110) REVERT: A 728 ASN cc_start: 0.8417 (m110) cc_final: 0.7821 (m-40) REVERT: A 779 ASP cc_start: 0.7386 (p0) cc_final: 0.6800 (p0) REVERT: A 844 TYR cc_start: 0.8628 (m-80) cc_final: 0.8423 (m-80) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.0509 time to fit residues: 4.9496 Evaluate side-chains 57 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 841 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.194412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154594 restraints weight = 7401.807| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.43 r_work: 0.3272 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1486 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= 0.127 Angle : 0.543 6.818 10778 Z= 0.293 Chirality : 0.041 0.285 1299 Planarity : 0.004 0.046 1206 Dihedral : 22.338 179.234 1520 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.89 % Allowed : 12.31 % Favored : 86.80 % 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: 0.18 (0.29), residues: 852 helix: 0.53 (0.21), residues: 606 sheet: -0.51 (0.69), residues: 56 loop : -0.66 (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 0.005 0.001 PHE A 797 TRP 0.003 0.000 TRP A 96 HIS 0.003 0.000 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 7728) covalent geometry : angle 0.54259 / 0.29 (10778) hydrogen bonds : bond 0.02924 / 2.03 ( 408) hydrogen bonds : angle 4.10938 / 2.95 ( 1171) metal coordination : bond 0.00164 / 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 58 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.230 Fit side-chains REVERT: A 125 LEU cc_start: 0.7498 (mt) cc_final: 0.7086 (mt) REVERT: A 728 ASN cc_start: 0.8385 (m110) cc_final: 0.7773 (m-40) REVERT: A 779 ASP cc_start: 0.7404 (p0) cc_final: 0.6819 (p0) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.0411 time to fit residues: 3.9285 Evaluate side-chains 57 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.0020 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 14 optimal weight: 0.0370 chunk 40 optimal weight: 0.0980 overall best weight: 0.3466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 627 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.191639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150643 restraints weight = 7457.706| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.62 r_work: 0.3219 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7731 Z= 0.114 Angle : 0.525 6.798 10778 Z= 0.285 Chirality : 0.040 0.282 1299 Planarity : 0.004 0.045 1206 Dihedral : 22.201 179.301 1520 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.74 % Allowed : 12.61 % 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: 0.30 (0.29), residues: 852 helix: 0.67 (0.22), residues: 599 sheet: -0.31 (0.70), residues: 54 loop : -0.81 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 810 TYR 0.016 0.001 TYR A 697 PHE 0.004 0.000 PHE A 797 TRP 0.003 0.000 TRP A 96 HIS 0.002 0.000 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 7728) covalent geometry : angle 0.52471 / 0.29 (10778) hydrogen bonds : bond 0.02686 / 1.86 ( 408) hydrogen bonds : angle 4.03980 / 2.91 ( 1171) metal coordination : bond 0.00141 / 0.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1508.15 seconds wall clock time: 26 minutes 33.87 seconds (1593.87 seconds total)