Starting phenix.real_space_refine on Fri Aug 22 16:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7urc_26708/08_2025/7urc_26708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urc_26708/08_2025/7urc_26708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7urc_26708/08_2025/7urc_26708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urc_26708/08_2025/7urc_26708.map" model { file = "/net/cci-nas-00/data/ceres_data/7urc_26708/08_2025/7urc_26708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urc_26708/08_2025/7urc_26708.cif" } resolution = 3.14 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= 0.008 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 31 5.16 5 C 3718 2.51 5 N 868 2.21 5 O 943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5561 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3449 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 357 Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 9, 'O50': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2833 SG CYS A 370 54.567 29.769 19.702 1.00119.07 S ATOM 2880 SG CYS A 376 53.579 28.925 23.636 1.00124.43 S ATOM 2908 SG CYS A 380 57.213 30.122 21.402 1.00134.93 S Time building chain proxies: 1.42, per 1000 atoms: 0.26 Number of scatterers: 5561 At special positions: 0 Unit cell: (97.11, 73.04, 93.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 31 16.00 O 943 8.00 N 868 7.00 C 3718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.02 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 232.4 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 512 " pdb="ZN ZN A 512 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 512 " - pdb=" SG CYS A 380 " pdb="ZN ZN A 512 " - pdb=" SG CYS A 370 " pdb="ZN ZN A 512 " - pdb=" SG CYS A 376 " Number of angles added : 3 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 7 sheets defined 52.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 removed outlier: 3.988A pdb=" N GLN A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 43 removed outlier: 3.744A pdb=" N ALA A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 34 " --> pdb=" O TRP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 68 Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.400A pdb=" N LEU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 116 through 141 removed outlier: 4.567A pdb=" N LYS A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ALA A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 172 through 181 removed outlier: 4.017A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.926A pdb=" N LEU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.833A pdb=" N TYR A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 264 removed outlier: 3.531A pdb=" N ALA A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.661A pdb=" N ASN A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.661A pdb=" N VAL A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 368 removed outlier: 3.961A pdb=" N ALA A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 409 Processing helix chain 'A' and resid 410 through 413 removed outlier: 4.061A pdb=" N ASP A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 455 removed outlier: 3.886A pdb=" N PHE A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 removed outlier: 3.663A pdb=" N THR H 84 " --> pdb=" O GLN H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.975A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AA3, first strand: chain 'L' and resid 30 through 32 removed outlier: 6.970A pdb=" N LEU L 31 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.417A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET H 53 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.417A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.19: 5 1.19 - 1.39: 2276 1.39 - 1.58: 3413 1.58 - 1.78: 8 1.78 - 1.98: 48 Bond restraints: 5750 Sorted by residual: bond pdb=" C07 AJP A 511 " pdb=" C08 AJP A 511 " ideal model delta sigma weight residual 1.550 1.978 -0.428 2.00e-02 2.50e+03 4.59e+02 bond pdb=" C01 AJP A 511 " pdb=" C02 AJP A 511 " ideal model delta sigma weight residual 1.521 1.943 -0.422 2.00e-02 2.50e+03 4.46e+02 bond pdb=" C08 AJP A 511 " pdb=" O09 AJP A 511 " ideal model delta sigma weight residual 1.410 0.995 0.415 2.00e-02 2.50e+03 4.31e+02 bond pdb=" C02 AJP A 511 " pdb=" C03 AJP A 511 " ideal model delta sigma weight residual 1.525 1.136 0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" C05 AJP A 511 " pdb=" O09 AJP A 511 " ideal model delta sigma weight residual 1.407 1.794 -0.387 2.00e-02 2.50e+03 3.74e+02 ... (remaining 5745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 7603 2.49 - 4.98: 217 4.98 - 7.47: 50 7.47 - 9.96: 11 9.96 - 12.44: 5 Bond angle restraints: 7886 Sorted by residual: angle pdb=" C03 AJP A 511 " pdb=" C02 AJP A 511 " pdb=" C85 AJP A 511 " ideal model delta sigma weight residual 109.14 121.58 -12.44 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C07 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C13 AJP A 511 " ideal model delta sigma weight residual 114.18 126.51 -12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C10 AJP A 511 " pdb=" C08 AJP A 511 " pdb=" O09 AJP A 511 " ideal model delta sigma weight residual 114.16 124.94 -10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C11 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C13 AJP A 511 " ideal model delta sigma weight residual 106.34 116.70 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C11 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C81 AJP A 511 " ideal model delta sigma weight residual 114.35 104.10 10.25 3.00e+00 1.11e-01 1.17e+01 ... (remaining 7881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 3688 35.39 - 70.77: 71 70.77 - 106.16: 33 106.16 - 141.54: 51 141.54 - 176.93: 8 Dihedral angle restraints: 3851 sinusoidal: 1944 harmonic: 1907 Sorted by residual: dihedral pdb=" CB CYS A 17 " pdb=" SG CYS A 17 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual -86.00 -158.72 72.72 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CA TYR H 74 " pdb=" C TYR H 74 " pdb=" N VAL H 75 " pdb=" CA VAL H 75 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" C06 AJP A 511 " pdb=" C07 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C13 AJP A 511 " ideal model delta sinusoidal sigma weight residual 109.15 -67.78 176.93 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.097: 883 1.097 - 2.193: 0 2.193 - 3.290: 0 3.290 - 4.386: 2 4.386 - 5.483: 27 Chirality restraints: 912 Sorted by residual: chirality pdb=" C20 AJP A 511 " pdb=" C15 AJP A 511 " pdb=" C19 AJP A 511 " pdb=" C21 AJP A 511 " both_signs ideal model delta sigma weight residual False 2.96 -2.53 5.48 2.00e-01 2.50e+01 7.52e+02 chirality pdb=" C16 AJP A 511 " pdb=" C11 AJP A 511 " pdb=" C15 AJP A 511 " pdb=" C17 AJP A 511 " both_signs ideal model delta sigma weight residual False -2.70 2.76 -5.46 2.00e-01 2.50e+01 7.47e+02 chirality pdb=" C15 AJP A 511 " pdb=" C14 AJP A 511 " pdb=" C16 AJP A 511 " pdb=" C20 AJP A 511 " both_signs ideal model delta sigma weight residual False -2.42 2.85 -5.27 2.00e-01 2.50e+01 6.95e+02 ... (remaining 909 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 376 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C CYS A 376 " -0.056 2.00e-02 2.50e+03 pdb=" O CYS A 376 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO A 377 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 219 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 220 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 375 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C ARG A 375 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG A 375 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 376 " -0.010 2.00e-02 2.50e+03 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1288 2.78 - 3.31: 5100 3.31 - 3.84: 9015 3.84 - 4.37: 10719 4.37 - 4.90: 18577 Nonbonded interactions: 44699 Sorted by model distance: nonbonded pdb=" O62 AJP A 511 " pdb=" O63 AJP A 511 " model vdw 2.248 3.040 nonbonded pdb=" O42 AJP A 511 " pdb=" O43 AJP A 511 " model vdw 2.263 3.040 nonbonded pdb=" NH1 ARG A 183 " pdb=" OE1 GLU A 270 " model vdw 2.306 3.120 nonbonded pdb=" NH1 ARG A 360 " pdb=" O LEU A 372 " model vdw 2.334 3.120 nonbonded pdb=" O SER H 138 " pdb=" OG SER H 138 " model vdw 2.350 3.040 ... (remaining 44694 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.510 Find NCS groups from input model: 0.010 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.021 0.880 5758 Z= 1.453 Angle : 1.081 26.669 7895 Z= 0.420 Chirality : 0.881 5.483 912 Planarity : 0.005 0.047 898 Dihedral : 25.593 176.927 2624 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -3.02 (0.29), residues: 648 helix: -1.25 (0.26), residues: 324 sheet: -2.18 (0.43), residues: 105 loop : -2.85 (0.35), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 318 TYR 0.013 0.001 TYR A 83 PHE 0.012 0.001 PHE A 167 TRP 0.008 0.001 TRP A 300 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.01752 ( 5750) covalent geometry : angle 1.00065 ( 7886) SS BOND : bond 0.00505 ( 3) SS BOND : angle 2.40252 ( 6) hydrogen bonds : bond 0.11577 ( 289) hydrogen bonds : angle 6.50840 ( 834) metal coordination : bond 0.08087 ( 4) metal coordination : angle 20.72802 ( 3) Misc. bond : bond 0.88006 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.131 Fit side-chains REVERT: A 191 GLN cc_start: 0.7938 (tt0) cc_final: 0.7545 (mt0) REVERT: A 235 ARG cc_start: 0.6878 (mmt180) cc_final: 0.5742 (mtm-85) REVERT: A 386 LEU cc_start: 0.9003 (pt) cc_final: 0.8725 (mp) REVERT: A 453 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7377 (ttt180) REVERT: L 65 GLN cc_start: 0.7427 (mt0) cc_final: 0.6843 (mm-40) REVERT: L 72 LYS cc_start: 0.9082 (ptpt) cc_final: 0.8712 (ptmm) REVERT: L 81 ARG cc_start: 0.8592 (ptt-90) cc_final: 0.8042 (ptt-90) REVERT: H 38 LYS cc_start: 0.9157 (tttt) cc_final: 0.8893 (tttp) REVERT: H 62 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8261 (mmmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0916 time to fit residues: 12.9230 Evaluate side-chains 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 24 GLN A 121 HIS A 247 HIS L 111 HIS H 24 GLN H 52 ASN H 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087851 restraints weight = 7657.576| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.50 r_work: 0.2917 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5758 Z= 0.131 Angle : 1.141 32.458 7895 Z= 0.426 Chirality : 0.118 2.187 912 Planarity : 0.004 0.045 898 Dihedral : 17.872 176.698 1501 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.43 % Allowed : 8.94 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -1.28 (0.32), residues: 648 helix: 0.34 (0.29), residues: 331 sheet: -1.94 (0.44), residues: 110 loop : -2.03 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.020 0.001 TYR A 83 PHE 0.011 0.001 PHE A 68 TRP 0.009 0.001 TRP A 120 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5750) covalent geometry : angle 1.13932 ( 7886) SS BOND : bond 0.00461 ( 3) SS BOND : angle 1.36677 ( 6) hydrogen bonds : bond 0.03070 ( 289) hydrogen bonds : angle 4.45451 ( 834) metal coordination : bond 0.01106 ( 4) metal coordination : angle 3.06356 ( 3) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.193 Fit side-chains REVERT: A 112 MET cc_start: 0.8170 (ptp) cc_final: 0.7802 (ptt) REVERT: A 188 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7083 (mtp85) REVERT: A 191 GLN cc_start: 0.7994 (tt0) cc_final: 0.7637 (mt0) REVERT: A 235 ARG cc_start: 0.7233 (mmt180) cc_final: 0.6609 (ptt-90) REVERT: A 386 LEU cc_start: 0.9009 (pt) cc_final: 0.8595 (mp) REVERT: A 453 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7141 (ttt180) REVERT: L 72 LYS cc_start: 0.8984 (ptpt) cc_final: 0.8541 (ptmm) REVERT: L 81 ARG cc_start: 0.8429 (ptt-90) cc_final: 0.8057 (ptt-90) REVERT: L 98 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7042 (mp) REVERT: H 38 LYS cc_start: 0.8975 (tttt) cc_final: 0.8611 (tttp) REVERT: H 62 LYS cc_start: 0.8485 (mmtm) cc_final: 0.7989 (mmmm) outliers start: 8 outliers final: 3 residues processed: 98 average time/residue: 0.0828 time to fit residues: 10.1592 Evaluate side-chains 96 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN H 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087138 restraints weight = 7478.940| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.36 r_work: 0.2943 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5758 Z= 0.159 Angle : 1.109 33.041 7895 Z= 0.417 Chirality : 0.118 2.213 912 Planarity : 0.004 0.044 898 Dihedral : 17.813 179.140 1501 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.07 % Allowed : 10.55 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -0.54 (0.33), residues: 648 helix: 1.00 (0.30), residues: 329 sheet: -1.76 (0.44), residues: 110 loop : -1.67 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.019 0.001 TYR A 83 PHE 0.010 0.001 PHE A 167 TRP 0.010 0.001 TRP A 300 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5750) covalent geometry : angle 1.10790 ( 7886) SS BOND : bond 0.00561 ( 3) SS BOND : angle 1.47508 ( 6) hydrogen bonds : bond 0.03085 ( 289) hydrogen bonds : angle 4.20476 ( 834) metal coordination : bond 0.00794 ( 4) metal coordination : angle 2.01464 ( 3) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.135 Fit side-chains REVERT: A 112 MET cc_start: 0.8287 (ptp) cc_final: 0.7872 (ptt) REVERT: A 188 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7186 (mtp85) REVERT: A 191 GLN cc_start: 0.8085 (tt0) cc_final: 0.7649 (mt0) REVERT: A 235 ARG cc_start: 0.7325 (mmt180) cc_final: 0.6693 (ptt-90) REVERT: A 386 LEU cc_start: 0.9019 (pt) cc_final: 0.8605 (mp) REVERT: A 436 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8389 (mm-30) REVERT: A 453 ARG cc_start: 0.7928 (ttt90) cc_final: 0.7271 (ttp-170) REVERT: L 72 LYS cc_start: 0.8983 (ptpt) cc_final: 0.8629 (ptmm) REVERT: L 81 ARG cc_start: 0.8545 (ptt-90) cc_final: 0.8034 (ptt-90) REVERT: H 38 LYS cc_start: 0.8976 (tttt) cc_final: 0.8641 (tttp) REVERT: H 62 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8022 (mmmm) outliers start: 6 outliers final: 3 residues processed: 94 average time/residue: 0.0792 time to fit residues: 9.4029 Evaluate side-chains 95 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.089105 restraints weight = 7567.353| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.59 r_work: 0.2920 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5758 Z= 0.118 Angle : 1.079 32.720 7895 Z= 0.401 Chirality : 0.116 2.148 912 Planarity : 0.004 0.043 898 Dihedral : 17.643 179.901 1501 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.25 % Allowed : 11.45 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: -0.08 (0.34), residues: 648 helix: 1.37 (0.30), residues: 329 sheet: -1.50 (0.46), residues: 110 loop : -1.47 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 117 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 167 TRP 0.008 0.001 TRP A 300 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5750) covalent geometry : angle 1.07851 ( 7886) SS BOND : bond 0.00467 ( 3) SS BOND : angle 1.24047 ( 6) hydrogen bonds : bond 0.02708 ( 289) hydrogen bonds : angle 3.93035 ( 834) metal coordination : bond 0.00388 ( 4) metal coordination : angle 1.51552 ( 3) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.198 Fit side-chains REVERT: A 112 MET cc_start: 0.8147 (ptp) cc_final: 0.7777 (ptt) REVERT: A 188 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7101 (mtp85) REVERT: A 191 GLN cc_start: 0.7972 (tt0) cc_final: 0.7600 (mt0) REVERT: A 235 ARG cc_start: 0.7209 (mmt180) cc_final: 0.5988 (mtm110) REVERT: A 386 LEU cc_start: 0.9055 (pt) cc_final: 0.8673 (mp) REVERT: A 436 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8043 (tt0) REVERT: A 453 ARG cc_start: 0.7826 (ttt90) cc_final: 0.7262 (ttp-170) REVERT: H 38 LYS cc_start: 0.8953 (tttt) cc_final: 0.8657 (tttp) REVERT: H 62 LYS cc_start: 0.8421 (mmtm) cc_final: 0.7891 (mmmm) REVERT: H 92 ASP cc_start: 0.7114 (t70) cc_final: 0.6889 (t70) REVERT: H 127 TYR cc_start: 0.8805 (m-80) cc_final: 0.8329 (m-80) outliers start: 7 outliers final: 4 residues processed: 95 average time/residue: 0.0796 time to fit residues: 9.5211 Evaluate side-chains 89 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain H residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.089493 restraints weight = 7755.317| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.62 r_work: 0.2978 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5758 Z= 0.113 Angle : 1.072 32.726 7895 Z= 0.396 Chirality : 0.115 2.133 912 Planarity : 0.004 0.041 898 Dihedral : 17.489 179.321 1501 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.07 % Allowed : 13.24 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: 0.21 (0.34), residues: 648 helix: 1.57 (0.30), residues: 329 sheet: -1.38 (0.47), residues: 111 loop : -1.25 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.017 0.001 TYR A 83 PHE 0.009 0.001 PHE A 340 TRP 0.007 0.001 TRP A 300 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5750) covalent geometry : angle 1.07199 ( 7886) SS BOND : bond 0.00332 ( 3) SS BOND : angle 1.24980 ( 6) hydrogen bonds : bond 0.02639 ( 289) hydrogen bonds : angle 3.83301 ( 834) metal coordination : bond 0.00412 ( 4) metal coordination : angle 1.43221 ( 3) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.169 Fit side-chains REVERT: A 112 MET cc_start: 0.8266 (ptp) cc_final: 0.7900 (ptt) REVERT: A 132 MET cc_start: 0.8297 (mtp) cc_final: 0.8058 (mtp) REVERT: A 188 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7161 (mmt-90) REVERT: A 191 GLN cc_start: 0.8075 (tt0) cc_final: 0.7726 (mt0) REVERT: A 235 ARG cc_start: 0.7313 (mmt180) cc_final: 0.6105 (mtm110) REVERT: A 386 LEU cc_start: 0.9135 (pt) cc_final: 0.8774 (mp) REVERT: A 436 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8170 (tt0) REVERT: A 453 ARG cc_start: 0.7820 (ttt90) cc_final: 0.7227 (ttp-170) REVERT: H 38 LYS cc_start: 0.8992 (tttt) cc_final: 0.8707 (tttp) REVERT: H 62 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8040 (mmmm) REVERT: H 127 TYR cc_start: 0.8891 (m-80) cc_final: 0.8473 (m-80) outliers start: 6 outliers final: 2 residues processed: 93 average time/residue: 0.0804 time to fit residues: 9.4686 Evaluate side-chains 88 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain H residue 30 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 18 optimal weight: 0.0170 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092152 restraints weight = 7578.224| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.55 r_work: 0.2918 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5758 Z= 0.092 Angle : 1.059 32.501 7895 Z= 0.389 Chirality : 0.114 2.108 912 Planarity : 0.004 0.040 898 Dihedral : 17.406 179.426 1501 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.72 % Allowed : 14.67 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: 0.57 (0.35), residues: 648 helix: 1.85 (0.30), residues: 330 sheet: -1.26 (0.48), residues: 113 loop : -1.04 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 6 TYR 0.021 0.001 TYR A 452 PHE 0.009 0.001 PHE A 340 TRP 0.010 0.001 TRP A 120 HIS 0.004 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 5750) covalent geometry : angle 1.05868 ( 7886) SS BOND : bond 0.00222 ( 3) SS BOND : angle 1.01461 ( 6) hydrogen bonds : bond 0.02376 ( 289) hydrogen bonds : angle 3.69811 ( 834) metal coordination : bond 0.00262 ( 4) metal coordination : angle 1.26422 ( 3) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.198 Fit side-chains REVERT: A 112 MET cc_start: 0.8127 (ptp) cc_final: 0.7790 (ptt) REVERT: A 132 MET cc_start: 0.7873 (mtp) cc_final: 0.7632 (mtm) REVERT: A 188 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6938 (mmt-90) REVERT: A 191 GLN cc_start: 0.7878 (tt0) cc_final: 0.7541 (mt0) REVERT: A 235 ARG cc_start: 0.7185 (mmt180) cc_final: 0.5931 (mtm110) REVERT: A 375 ARG cc_start: 0.5476 (mmt180) cc_final: 0.5196 (mmt180) REVERT: A 436 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8030 (tt0) REVERT: A 452 TYR cc_start: 0.8333 (t80) cc_final: 0.8094 (t80) REVERT: A 453 ARG cc_start: 0.7685 (ttt90) cc_final: 0.7027 (ttp-170) REVERT: L 81 ARG cc_start: 0.8375 (ptt-90) cc_final: 0.8101 (ptt-90) REVERT: H 38 LYS cc_start: 0.8824 (tttt) cc_final: 0.8526 (tttp) REVERT: H 62 LYS cc_start: 0.8368 (mmtm) cc_final: 0.7764 (mmmm) REVERT: H 92 ASP cc_start: 0.7013 (t70) cc_final: 0.6781 (t70) REVERT: H 127 TYR cc_start: 0.8725 (m-80) cc_final: 0.8141 (m-80) outliers start: 4 outliers final: 4 residues processed: 98 average time/residue: 0.0945 time to fit residues: 11.6300 Evaluate side-chains 93 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.0020 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090938 restraints weight = 7671.723| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.57 r_work: 0.2993 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5758 Z= 0.105 Angle : 1.062 32.625 7895 Z= 0.391 Chirality : 0.115 2.116 912 Planarity : 0.004 0.038 898 Dihedral : 17.380 179.680 1501 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.07 % Allowed : 14.67 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: 0.73 (0.35), residues: 648 helix: 1.97 (0.30), residues: 331 sheet: -1.06 (0.49), residues: 111 loop : -1.03 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 81 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 167 TRP 0.009 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 5750) covalent geometry : angle 1.06227 ( 7886) SS BOND : bond 0.00336 ( 3) SS BOND : angle 1.11439 ( 6) hydrogen bonds : bond 0.02479 ( 289) hydrogen bonds : angle 3.68710 ( 834) metal coordination : bond 0.00303 ( 4) metal coordination : angle 1.31806 ( 3) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.119 Fit side-chains REVERT: A 112 MET cc_start: 0.8197 (ptp) cc_final: 0.7849 (ptt) REVERT: A 132 MET cc_start: 0.8112 (mtp) cc_final: 0.7785 (mtm) REVERT: A 191 GLN cc_start: 0.7949 (tt0) cc_final: 0.7582 (mt0) REVERT: A 235 ARG cc_start: 0.7257 (mmt180) cc_final: 0.5955 (mtm110) REVERT: A 427 MET cc_start: 0.7416 (ttp) cc_final: 0.7212 (tmm) REVERT: A 436 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8093 (tt0) REVERT: A 453 ARG cc_start: 0.7671 (ttt90) cc_final: 0.7036 (ttp-170) REVERT: L 81 ARG cc_start: 0.8472 (ptt-90) cc_final: 0.8222 (ptt-90) REVERT: H 38 LYS cc_start: 0.8890 (tttt) cc_final: 0.8598 (tttp) REVERT: H 62 LYS cc_start: 0.8472 (mmtm) cc_final: 0.7869 (mmmm) REVERT: H 92 ASP cc_start: 0.7151 (t70) cc_final: 0.6915 (t70) REVERT: H 127 TYR cc_start: 0.8831 (m-80) cc_final: 0.8327 (m-80) outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 0.0755 time to fit residues: 9.3354 Evaluate side-chains 94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.090633 restraints weight = 7548.175| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.59 r_work: 0.2943 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5758 Z= 0.108 Angle : 1.063 32.592 7895 Z= 0.392 Chirality : 0.115 2.118 912 Planarity : 0.004 0.039 898 Dihedral : 17.352 179.713 1501 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.89 % Allowed : 15.74 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: 0.82 (0.35), residues: 648 helix: 2.01 (0.30), residues: 331 sheet: -0.95 (0.49), residues: 111 loop : -0.99 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 340 TRP 0.009 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5750) covalent geometry : angle 1.06308 ( 7886) SS BOND : bond 0.00316 ( 3) SS BOND : angle 1.06815 ( 6) hydrogen bonds : bond 0.02497 ( 289) hydrogen bonds : angle 3.67338 ( 834) metal coordination : bond 0.00311 ( 4) metal coordination : angle 1.42732 ( 3) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.271 Fit side-chains REVERT: A 112 MET cc_start: 0.8185 (ptp) cc_final: 0.7842 (ptt) REVERT: A 132 MET cc_start: 0.8058 (mtp) cc_final: 0.7798 (mtp) REVERT: A 191 GLN cc_start: 0.7913 (tt0) cc_final: 0.7565 (mt0) REVERT: A 235 ARG cc_start: 0.7199 (mmt180) cc_final: 0.5875 (mtm110) REVERT: A 375 ARG cc_start: 0.5693 (mmt180) cc_final: 0.5210 (mmt90) REVERT: A 436 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8068 (tt0) REVERT: A 453 ARG cc_start: 0.7632 (ttt90) cc_final: 0.7006 (ttp-170) REVERT: H 38 LYS cc_start: 0.8853 (tttt) cc_final: 0.8565 (tttp) REVERT: H 62 LYS cc_start: 0.8438 (mmtm) cc_final: 0.7823 (mmmm) REVERT: H 92 ASP cc_start: 0.7065 (t70) cc_final: 0.6829 (t70) REVERT: H 127 TYR cc_start: 0.8795 (m-80) cc_final: 0.8276 (m-80) outliers start: 5 outliers final: 4 residues processed: 96 average time/residue: 0.0753 time to fit residues: 9.5558 Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.088592 restraints weight = 7700.230| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.55 r_work: 0.2970 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5758 Z= 0.138 Angle : 1.075 32.781 7895 Z= 0.400 Chirality : 0.115 2.138 912 Planarity : 0.004 0.039 898 Dihedral : 17.359 179.890 1501 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.25 % Allowed : 15.56 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: 0.79 (0.35), residues: 648 helix: 1.96 (0.29), residues: 332 sheet: -0.95 (0.49), residues: 111 loop : -0.97 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.018 0.001 TYR A 452 PHE 0.010 0.001 PHE A 167 TRP 0.017 0.001 TRP A 120 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5750) covalent geometry : angle 1.07477 ( 7886) SS BOND : bond 0.00220 ( 3) SS BOND : angle 1.43044 ( 6) hydrogen bonds : bond 0.02739 ( 289) hydrogen bonds : angle 3.77287 ( 834) metal coordination : bond 0.00458 ( 4) metal coordination : angle 1.60203 ( 3) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.211 Fit side-chains REVERT: A 112 MET cc_start: 0.8258 (ptp) cc_final: 0.7888 (ptt) REVERT: A 191 GLN cc_start: 0.8008 (tt0) cc_final: 0.7660 (mt0) REVERT: A 235 ARG cc_start: 0.7232 (mmt180) cc_final: 0.5881 (mtm110) REVERT: A 375 ARG cc_start: 0.5645 (mmt180) cc_final: 0.5124 (mmt90) REVERT: A 436 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8109 (tt0) REVERT: A 453 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7016 (ttp-170) REVERT: L 98 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7263 (mp) REVERT: H 38 LYS cc_start: 0.8916 (tttt) cc_final: 0.8632 (tttp) REVERT: H 62 LYS cc_start: 0.8513 (mmtm) cc_final: 0.7910 (mmmm) REVERT: H 92 ASP cc_start: 0.7203 (t70) cc_final: 0.6998 (t70) outliers start: 7 outliers final: 4 residues processed: 93 average time/residue: 0.0794 time to fit residues: 9.4073 Evaluate side-chains 93 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.091511 restraints weight = 7590.496| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.43 r_work: 0.2920 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5758 Z= 0.096 Angle : 1.058 32.401 7895 Z= 0.389 Chirality : 0.115 2.114 912 Planarity : 0.004 0.038 898 Dihedral : 17.335 179.754 1501 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.89 % Allowed : 16.10 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: 0.92 (0.35), residues: 648 helix: 2.08 (0.30), residues: 332 sheet: -0.90 (0.50), residues: 111 loop : -0.92 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 340 TRP 0.018 0.001 TRP A 120 HIS 0.003 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 5750) covalent geometry : angle 1.05734 ( 7886) SS BOND : bond 0.00279 ( 3) SS BOND : angle 1.07335 ( 6) hydrogen bonds : bond 0.02432 ( 289) hydrogen bonds : angle 3.64250 ( 834) metal coordination : bond 0.00285 ( 4) metal coordination : angle 1.46973 ( 3) Misc. bond : bond 0.00012 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.188 Fit side-chains REVERT: A 112 MET cc_start: 0.8160 (ptp) cc_final: 0.7808 (ptt) REVERT: A 132 MET cc_start: 0.8076 (mtp) cc_final: 0.7795 (mtm) REVERT: A 191 GLN cc_start: 0.7961 (tt0) cc_final: 0.7606 (mt0) REVERT: A 235 ARG cc_start: 0.7261 (mmt180) cc_final: 0.5814 (mtm110) REVERT: A 375 ARG cc_start: 0.5789 (mmt180) cc_final: 0.5316 (mmt90) REVERT: A 436 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8084 (tt0) REVERT: A 453 ARG cc_start: 0.7609 (ttt90) cc_final: 0.6862 (ttp-170) REVERT: L 98 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7021 (mp) REVERT: H 38 LYS cc_start: 0.8799 (tttt) cc_final: 0.8503 (tttp) REVERT: H 62 LYS cc_start: 0.8374 (mmtm) cc_final: 0.7748 (mmmm) REVERT: H 92 ASP cc_start: 0.6919 (t70) cc_final: 0.6695 (t70) REVERT: H 127 TYR cc_start: 0.8780 (m-80) cc_final: 0.8249 (m-80) outliers start: 5 outliers final: 4 residues processed: 94 average time/residue: 0.0738 time to fit residues: 9.0085 Evaluate side-chains 93 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 54 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.0070 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091406 restraints weight = 7605.837| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.55 r_work: 0.2908 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5758 Z= 0.102 Angle : 1.059 32.569 7895 Z= 0.390 Chirality : 0.115 2.116 912 Planarity : 0.004 0.038 898 Dihedral : 17.332 179.828 1501 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.89 % Allowed : 15.92 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 aren not related in a simple way. whole: 0.98 (0.35), residues: 648 helix: 2.13 (0.30), residues: 331 sheet: -0.81 (0.50), residues: 111 loop : -0.94 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.017 0.001 TYR A 83 PHE 0.008 0.001 PHE A 167 TRP 0.017 0.001 TRP A 120 HIS 0.003 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 5750) covalent geometry : angle 1.05871 ( 7886) SS BOND : bond 0.00300 ( 3) SS BOND : angle 1.13213 ( 6) hydrogen bonds : bond 0.02462 ( 289) hydrogen bonds : angle 3.63889 ( 834) metal coordination : bond 0.00317 ( 4) metal coordination : angle 1.44795 ( 3) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.87 seconds wall clock time: 21 minutes 22.00 seconds (1282.00 seconds total)