Starting phenix.real_space_refine on Tue Feb 3 23:20:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lcx_62995/02_2026/9lcx_62995.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lcx_62995/02_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_62995/02_2026/9lcx_62995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lcx_62995/02_2026/9lcx_62995.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lcx_62995/02_2026/9lcx_62995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lcx_62995/02_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-2.0-5952/lib/python3.9/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: 1.87, per 1000 atoms: 0.25 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: 0.81 Conformation dependent library (CDL) restraints added in 264.7 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: 1.02 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: 1.57 Time building geometry restraints manager: 1.01 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=" C PRO A 115 " pdb=" N PRO A 116 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.87e+00 bond pdb=" C3' DG C 2 " pdb=" O3' DG C 2 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C LEU A 552 " pdb=" N PRO A 553 " ideal model delta sigma weight residual 1.334 1.344 -0.010 8.40e-03 1.42e+04 1.42e+00 bond pdb=" C3' DT C -4 " pdb=" O3' DT C -4 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" O4' DT B -17 " pdb=" C1' DT B -17 " ideal model delta sigma weight residual 1.414 1.392 0.022 2.00e-02 2.50e+03 1.18e+00 ... (remaining 7723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 10239 1.20 - 2.41: 453 2.41 - 3.61: 62 3.61 - 4.81: 19 4.81 - 6.01: 5 Bond angle restraints: 10778 Sorted by residual: angle pdb=" N ILE A 771 " pdb=" CA ILE A 771 " pdb=" C ILE A 771 " ideal model delta sigma weight residual 111.48 108.63 2.85 9.40e-01 1.13e+00 9.22e+00 angle pdb=" C TYR A 834 " pdb=" N HIS A 835 " pdb=" CA HIS A 835 " ideal model delta sigma weight residual 123.32 119.17 4.15 1.88e+00 2.83e-01 4.87e+00 angle pdb=" CA LEU A 348 " pdb=" C LEU A 348 " pdb=" N PRO A 349 " ideal model delta sigma weight residual 118.44 121.78 -3.34 1.59e+00 3.96e-01 4.42e+00 angle pdb=" C3' DG C 2 " pdb=" O3' DG C 2 " pdb=" P DG C 3 " ideal model delta sigma weight residual 120.20 123.32 -3.12 1.50e+00 4.44e-01 4.34e+00 angle pdb=" C SER A 770 " pdb=" N ILE A 771 " pdb=" CA ILE A 771 " ideal model delta sigma weight residual 122.97 120.97 2.00 9.80e-01 1.04e+00 4.17e+00 ... (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 - 0.026: 718 0.026 - 0.052: 338 0.052 - 0.078: 152 0.078 - 0.104: 71 0.104 - 0.130: 20 Chirality restraints: 1299 Sorted by residual: 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=" CA PRO A 427 " pdb=" N PRO A 427 " pdb=" C PRO A 427 " pdb=" CB PRO A 427 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 32 " pdb=" N ILE A 32 " pdb=" C ILE A 32 " pdb=" CB ILE A 32 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.27e-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: 1.220 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.005 0.214 7731 Z= 0.205 Angle : 0.584 6.015 10778 Z= 0.329 Chirality : 0.040 0.130 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 covalent geometry : bond 0.00439 ( 7728) covalent geometry : angle 0.58446 (10778) hydrogen bonds : bond 0.15821 ( 408) hydrogen bonds : angle 6.80362 ( 1171) metal coordination : bond 0.12374 ( 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 : 0.248 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: 0.0696 time to fit residues: 5.3433 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 : 0.242 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 559 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 = 0.4114 r_free = 0.4114 target = 0.194326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.154106 restraints weight = 7390.856| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.44 r_work: 0.3255 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7731 Z= 0.134 Angle : 0.537 5.840 10778 Z= 0.293 Chirality : 0.039 0.152 1299 Planarity : 0.005 0.046 1206 Dihedral : 21.581 178.389 1520 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -0.44 (0.29), residues: 852 helix: 0.01 (0.21), residues: 605 sheet: -0.83 (0.68), residues: 54 loop : -0.59 (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 0.005 0.001 PHE A 797 TRP 0.004 0.001 TRP A 96 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7728) covalent geometry : angle 0.53725 (10778) hydrogen bonds : bond 0.03193 ( 408) hydrogen bonds : angle 4.41826 ( 1171) metal coordination : bond 0.00471 ( 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 53 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.252 Fit side-chains REVERT: A 125 LEU cc_start: 0.7556 (mt) cc_final: 0.7146 (mt) REVERT: A 216 CYS cc_start: 0.7604 (m) cc_final: 0.7308 (t) REVERT: A 625 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7291 (mm-40) REVERT: A 724 ASN cc_start: 0.7875 (t0) cc_final: 0.7491 (t0) REVERT: A 835 HIS cc_start: 0.7709 (p90) cc_final: 0.7464 (p90) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.0544 time to fit residues: 4.7403 Evaluate side-chains 51 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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: 4.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4095 r_free = 0.4095 target = 0.192028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.161855 restraints weight = 7334.641| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 0.91 r_work: 0.3331 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7731 Z= 0.168 Angle : 0.558 5.784 10778 Z= 0.299 Chirality : 0.040 0.129 1299 Planarity : 0.005 0.047 1206 Dihedral : 21.874 176.694 1520 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.45 % Allowed : 6.97 % Favored : 92.58 % 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: -0.24 (0.29), residues: 852 helix: 0.18 (0.21), residues: 603 sheet: -0.85 (0.67), residues: 56 loop : -0.56 (0.47), residues: 193 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 0.007 0.001 PHE A 797 TRP 0.003 0.001 TRP A 96 HIS 0.003 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7728) covalent geometry : angle 0.55826 (10778) hydrogen bonds : bond 0.03376 ( 408) hydrogen bonds : angle 4.34503 ( 1171) metal coordination : bond 0.00284 ( 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 : 0.249 Fit side-chains REVERT: A 125 LEU cc_start: 0.7596 (mt) cc_final: 0.7169 (mt) REVERT: A 724 ASN cc_start: 0.7898 (t0) cc_final: 0.7569 (t0) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.0588 time to fit residues: 4.9716 Evaluate side-chains 48 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4097 r_free = 0.4097 target = 0.192285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.160254 restraints weight = 7506.498| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 0.99 r_work: 0.3328 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7731 Z= 0.162 Angle : 0.546 6.487 10778 Z= 0.292 Chirality : 0.039 0.128 1299 Planarity : 0.005 0.048 1206 Dihedral : 21.922 176.450 1520 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.74 % Allowed : 8.61 % Favored : 90.65 % 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: -0.07 (0.29), residues: 852 helix: 0.31 (0.21), residues: 603 sheet: -0.65 (0.69), residues: 54 loop : -0.55 (0.47), residues: 195 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 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7728) covalent geometry : angle 0.54583 (10778) hydrogen bonds : bond 0.03196 ( 408) hydrogen bonds : angle 4.25851 ( 1171) metal coordination : bond 0.00254 ( 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 58 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.181 Fit side-chains REVERT: A 125 LEU cc_start: 0.7641 (mt) cc_final: 0.7196 (mt) REVERT: A 216 CYS cc_start: 0.7502 (m) cc_final: 0.7222 (t) REVERT: A 724 ASN cc_start: 0.7940 (t0) cc_final: 0.7620 (t0) outliers start: 5 outliers final: 2 residues processed: 58 average time/residue: 0.0495 time to fit residues: 4.6649 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 : 0.210 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 2 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 243 GLN A 339 GLN A 593 HIS A 835 HIS A 836 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.193124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154101 restraints weight = 7483.244| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.52 r_work: 0.3260 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7731 Z= 0.117 Angle : 0.491 6.947 10778 Z= 0.265 Chirality : 0.037 0.121 1299 Planarity : 0.004 0.046 1206 Dihedral : 21.323 176.723 1520 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.45 % Allowed : 9.94 % Favored : 89.61 % 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: 0.34 (0.30), residues: 852 helix: 0.67 (0.22), residues: 598 sheet: -0.48 (0.71), residues: 56 loop : -0.59 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 312 TYR 0.013 0.001 TYR A 697 PHE 0.003 0.000 PHE A 797 TRP 0.002 0.000 TRP A 96 HIS 0.002 0.000 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7728) covalent geometry : angle 0.49070 (10778) hydrogen bonds : bond 0.02476 ( 408) hydrogen bonds : angle 3.98159 ( 1171) metal coordination : bond 0.00268 ( 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 60 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.194 Fit side-chains REVERT: A 125 LEU cc_start: 0.7481 (mt) cc_final: 0.7035 (mt) REVERT: A 216 CYS cc_start: 0.7423 (m) cc_final: 0.7217 (t) REVERT: A 339 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8626 (mm110) outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 0.0541 time to fit residues: 5.2293 Evaluate side-chains 56 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.189793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151583 restraints weight = 7409.597| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.48 r_work: 0.3219 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7731 Z= 0.148 Angle : 0.529 7.407 10778 Z= 0.282 Chirality : 0.039 0.126 1299 Planarity : 0.004 0.047 1206 Dihedral : 21.636 176.819 1520 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.59 % Allowed : 10.53 % Favored : 88.87 % 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: 0.26 (0.29), residues: 852 helix: 0.62 (0.22), residues: 600 sheet: -0.32 (0.72), residues: 54 loop : -0.75 (0.46), residues: 198 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 0.006 0.001 PHE A 797 TRP 0.002 0.001 TRP A 96 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7728) covalent geometry : angle 0.52886 (10778) hydrogen bonds : bond 0.02888 ( 408) hydrogen bonds : angle 4.08311 ( 1171) metal coordination : bond 0.00236 ( 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 62 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.160 Fit side-chains REVERT: A 125 LEU cc_start: 0.7540 (mt) cc_final: 0.7080 (mt) REVERT: A 779 ASP cc_start: 0.7702 (p0) cc_final: 0.7091 (p0) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.0498 time to fit residues: 4.9364 Evaluate side-chains 59 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 LEU 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: 1.9990 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.188782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.150394 restraints weight = 7464.884| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.44 r_work: 0.3202 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7731 Z= 0.164 Angle : 0.545 7.561 10778 Z= 0.290 Chirality : 0.039 0.128 1299 Planarity : 0.004 0.047 1206 Dihedral : 21.807 177.030 1520 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.89 % Allowed : 10.68 % Favored : 88.43 % 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: 0.11 (0.29), residues: 852 helix: 0.51 (0.21), residues: 603 sheet: -0.40 (0.71), residues: 54 loop : -0.83 (0.46), residues: 195 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 0.007 0.001 PHE A 797 TRP 0.003 0.000 TRP A 96 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7728) covalent geometry : angle 0.54533 (10778) hydrogen bonds : bond 0.03147 ( 408) hydrogen bonds : angle 4.16457 ( 1171) metal coordination : bond 0.00200 ( 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 64 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.158 Fit side-chains REVERT: A 625 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7298 (mm-40) REVERT: A 728 ASN cc_start: 0.8381 (m110) cc_final: 0.7736 (m-40) REVERT: A 779 ASP cc_start: 0.7655 (p0) cc_final: 0.7123 (p0) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.0501 time to fit residues: 5.0442 Evaluate side-chains 62 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4069 r_free = 0.4069 target = 0.189795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.149535 restraints weight = 7483.212| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.50 r_work: 0.3215 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7731 Z= 0.143 Angle : 0.525 7.965 10778 Z= 0.280 Chirality : 0.038 0.127 1299 Planarity : 0.004 0.047 1206 Dihedral : 21.688 177.449 1520 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.89 % Allowed : 11.13 % Favored : 87.98 % 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: 0.59 (0.21), residues: 601 sheet: -0.49 (0.69), residues: 56 loop : -0.83 (0.46), residues: 195 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 0.006 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7728) covalent geometry : angle 0.52513 (10778) hydrogen bonds : bond 0.02917 ( 408) hydrogen bonds : angle 4.10163 ( 1171) metal coordination : bond 0.00174 ( 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 61 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.248 Fit side-chains REVERT: A 125 LEU cc_start: 0.7482 (mt) cc_final: 0.7108 (mt) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.0443 time to fit residues: 4.3331 Evaluate side-chains 60 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 48 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.189942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151711 restraints weight = 7424.464| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.49 r_work: 0.3223 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7731 Z= 0.140 Angle : 0.527 7.857 10778 Z= 0.281 Chirality : 0.039 0.126 1299 Planarity : 0.004 0.047 1206 Dihedral : 21.634 177.716 1520 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 0.24 (0.29), residues: 852 helix: 0.64 (0.21), residues: 599 sheet: -0.46 (0.69), residues: 56 loop : -0.83 (0.46), residues: 197 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 0.004 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7728) covalent geometry : angle 0.52732 (10778) hydrogen bonds : bond 0.02898 ( 408) hydrogen bonds : angle 4.11013 ( 1171) metal coordination : bond 0.00165 ( 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: 5 poor density : 55 time to evaluate : 0.155 Fit side-chains REVERT: A 125 LEU cc_start: 0.7538 (mt) cc_final: 0.7152 (mt) REVERT: A 728 ASN cc_start: 0.8376 (m110) cc_final: 0.7784 (m110) REVERT: A 844 TYR cc_start: 0.8702 (m-80) cc_final: 0.8468 (m-80) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.0540 time to fit residues: 5.0901 Evaluate side-chains 60 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 24 optimal weight: 0.2980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.192210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151451 restraints weight = 7442.566| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.54 r_work: 0.3256 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7731 Z= 0.121 Angle : 0.504 7.786 10778 Z= 0.270 Chirality : 0.038 0.124 1299 Planarity : 0.004 0.046 1206 Dihedral : 21.398 178.217 1520 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.89 % Allowed : 11.13 % Favored : 87.98 % 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: 0.36 (0.29), residues: 852 helix: 0.73 (0.22), residues: 599 sheet: -0.20 (0.71), residues: 54 loop : -0.86 (0.46), residues: 199 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 0.000 PHE A 797 TRP 0.003 0.000 TRP A 96 HIS 0.009 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7728) covalent geometry : angle 0.50387 (10778) hydrogen bonds : bond 0.02554 ( 408) hydrogen bonds : angle 4.00980 ( 1171) metal coordination : bond 0.00137 ( 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 60 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.241 Fit side-chains REVERT: A 125 LEU cc_start: 0.7475 (mt) cc_final: 0.7096 (mt) REVERT: A 339 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8548 (mm110) REVERT: A 728 ASN cc_start: 0.8338 (m110) cc_final: 0.7729 (m110) REVERT: A 779 ASP cc_start: 0.7559 (p0) cc_final: 0.7302 (p0) REVERT: A 844 TYR cc_start: 0.8597 (m-80) cc_final: 0.8377 (m-80) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.0525 time to fit residues: 4.9144 Evaluate side-chains 59 residues out of total 674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR 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: 0.6980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 0.0020 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.186806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.148101 restraints weight = 7383.450| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.46 r_work: 0.3207 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7731 Z= 0.163 Angle : 0.533 8.265 10778 Z= 0.284 Chirality : 0.039 0.126 1299 Planarity : 0.004 0.047 1206 Dihedral : 21.539 178.134 1520 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 0.26 (0.29), residues: 852 helix: 0.65 (0.21), residues: 599 sheet: -0.23 (0.71), residues: 54 loop : -0.87 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 652 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 covalent geometry : bond 0.00389 ( 7728) covalent geometry : angle 0.53320 (10778) hydrogen bonds : bond 0.02947 ( 408) hydrogen bonds : angle 4.06580 ( 1171) metal coordination : bond 0.00229 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1499.47 seconds wall clock time: 26 minutes 24.33 seconds (1584.33 seconds total)