Starting phenix.real_space_refine on Thu Jul 24 11:22:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7urc_26708/07_2025/7urc_26708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urc_26708/07_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_26708/07_2025/7urc_26708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urc_26708/07_2025/7urc_26708.map" model { file = "/net/cci-nas-00/data/ceres_data/7urc_26708/07_2025/7urc_26708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urc_26708/07_2025/7urc_26708.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'HIS:plan': 1, 'ASP: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: 5.03, per 1000 atoms: 0.90 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: 2.36 Conformation dependent library (CDL) restraints added in 883.9 milliseconds 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: 0.67 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: 1.67 Time building geometry restraints manager: 2.27 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: 7.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.770 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: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- 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 : 10.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 300 HIS 0.004 0.001 HIS A 341 PHE 0.012 0.001 PHE A 167 TYR 0.013 0.001 TYR A 83 ARG 0.002 0.000 ARG A 318 Details of bonding type rmsd hydrogen bonds : bond 0.11577 ( 289) hydrogen bonds : angle 6.50840 ( 834) metal coordination : bond 0.08087 ( 4) metal coordination : angle 20.72802 ( 3) SS BOND : bond 0.00505 ( 3) SS BOND : angle 2.40252 ( 6) covalent geometry : bond 0.01752 ( 5750) covalent geometry : angle 1.00065 ( 7886) 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 : 0.650 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: 0.3203 time to fit residues: 45.4467 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 : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.085625 restraints weight = 7629.772| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.45 r_work: 0.2879 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5758 Z= 0.188 Angle : 1.158 33.536 7895 Z= 0.438 Chirality : 0.120 2.238 912 Planarity : 0.004 0.046 898 Dihedral : 17.964 176.706 1501 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.25 % Allowed : 10.02 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.32), residues: 648 helix: 0.23 (0.28), residues: 332 sheet: -2.04 (0.43), residues: 111 loop : -2.10 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 300 HIS 0.006 0.001 HIS A 53 PHE 0.012 0.001 PHE A 68 TYR 0.021 0.001 TYR A 83 ARG 0.005 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 289) hydrogen bonds : angle 4.58249 ( 834) metal coordination : bond 0.01286 ( 4) metal coordination : angle 3.48097 ( 3) SS BOND : bond 0.00560 ( 3) SS BOND : angle 1.64669 ( 6) covalent geometry : bond 0.00439 ( 5750) covalent geometry : angle 1.15564 ( 7886) Misc. bond : bond 0.00231 ( 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 98 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.627 Fit side-chains REVERT: A 112 MET cc_start: 0.8280 (ptp) cc_final: 0.7840 (ptt) REVERT: A 188 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7163 (mtp85) REVERT: A 191 GLN cc_start: 0.8083 (tt0) cc_final: 0.7709 (mt0) REVERT: A 235 ARG cc_start: 0.7311 (mmt180) cc_final: 0.6702 (ptt-90) REVERT: A 386 LEU cc_start: 0.8980 (pt) cc_final: 0.8554 (mp) REVERT: A 453 ARG cc_start: 0.7982 (ttt90) cc_final: 0.7211 (ttt180) REVERT: L 56 TYR cc_start: 0.9397 (m-80) cc_final: 0.9115 (m-80) REVERT: L 72 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8653 (ptmm) REVERT: L 81 ARG cc_start: 0.8586 (ptt-90) cc_final: 0.8132 (ptt-90) REVERT: L 98 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7263 (mp) REVERT: H 38 LYS cc_start: 0.8991 (tttt) cc_final: 0.8654 (tttp) REVERT: H 62 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8080 (mmmm) outliers start: 7 outliers final: 2 residues processed: 93 average time/residue: 0.2337 time to fit residues: 27.0036 Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL 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 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.0270 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.116603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.089250 restraints weight = 7472.104| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.37 r_work: 0.2929 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5758 Z= 0.112 Angle : 1.088 32.402 7895 Z= 0.404 Chirality : 0.117 2.189 912 Planarity : 0.004 0.044 898 Dihedral : 17.779 179.643 1501 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.33), residues: 648 helix: 1.08 (0.30), residues: 329 sheet: -1.76 (0.44), residues: 110 loop : -1.71 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 300 HIS 0.004 0.001 HIS A 53 PHE 0.010 0.001 PHE A 340 TYR 0.017 0.001 TYR A 83 ARG 0.001 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 289) hydrogen bonds : angle 4.08508 ( 834) metal coordination : bond 0.00732 ( 4) metal coordination : angle 2.07795 ( 3) SS BOND : bond 0.00406 ( 3) SS BOND : angle 1.10298 ( 6) covalent geometry : bond 0.00254 ( 5750) covalent geometry : angle 1.08719 ( 7886) Misc. bond : bond 0.00103 ( 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 99 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.614 Fit side-chains REVERT: A 112 MET cc_start: 0.8168 (ptp) cc_final: 0.7799 (ptt) REVERT: A 132 MET cc_start: 0.8574 (mtp) cc_final: 0.8297 (mtp) REVERT: A 188 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7115 (mtp85) REVERT: A 191 GLN cc_start: 0.8035 (tt0) cc_final: 0.7659 (mt0) REVERT: A 235 ARG cc_start: 0.7298 (mmt180) cc_final: 0.6678 (ptt-90) REVERT: A 386 LEU cc_start: 0.9010 (pt) cc_final: 0.8599 (mp) REVERT: A 436 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 453 ARG cc_start: 0.7906 (ttt90) cc_final: 0.7252 (ttp-170) REVERT: L 81 ARG cc_start: 0.8521 (ptt-90) cc_final: 0.8079 (ptt-90) REVERT: H 38 LYS cc_start: 0.8979 (tttt) cc_final: 0.8652 (tttp) REVERT: H 62 LYS cc_start: 0.8509 (mmtm) cc_final: 0.7990 (mmmm) REVERT: H 127 TYR cc_start: 0.8872 (m-80) cc_final: 0.8378 (m-80) outliers start: 7 outliers final: 2 residues processed: 96 average time/residue: 0.3293 time to fit residues: 39.9521 Evaluate side-chains 96 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain L residue 21 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087404 restraints weight = 7753.460| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.58 r_work: 0.2940 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5758 Z= 0.146 Angle : 1.092 33.076 7895 Z= 0.408 Chirality : 0.116 2.172 912 Planarity : 0.004 0.043 898 Dihedral : 17.682 179.359 1501 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.79 % Allowed : 11.99 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.34), residues: 648 helix: 1.31 (0.30), residues: 330 sheet: -1.59 (0.46), residues: 111 loop : -1.43 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 300 HIS 0.004 0.001 HIS A 53 PHE 0.010 0.001 PHE A 167 TYR 0.019 0.001 TYR A 83 ARG 0.002 0.000 ARG H 117 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 289) hydrogen bonds : angle 4.01241 ( 834) metal coordination : bond 0.00636 ( 4) metal coordination : angle 1.79919 ( 3) SS BOND : bond 0.00539 ( 3) SS BOND : angle 1.50087 ( 6) covalent geometry : bond 0.00338 ( 5750) covalent geometry : angle 1.09098 ( 7886) Misc. bond : bond 0.00057 ( 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 101 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.577 Fit side-chains REVERT: A 92 SER cc_start: 0.8988 (t) cc_final: 0.8662 (t) REVERT: A 112 MET cc_start: 0.8261 (ptp) cc_final: 0.7888 (ptt) REVERT: A 188 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7302 (mtp85) REVERT: A 191 GLN cc_start: 0.8119 (tt0) cc_final: 0.7734 (mt0) REVERT: A 235 ARG cc_start: 0.7306 (mmt180) cc_final: 0.6131 (mtm110) REVERT: A 386 LEU cc_start: 0.9112 (pt) cc_final: 0.8733 (mp) REVERT: A 436 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8177 (tt0) REVERT: A 453 ARG cc_start: 0.7883 (ttt90) cc_final: 0.7334 (ttp-170) REVERT: H 38 LYS cc_start: 0.9031 (tttt) cc_final: 0.8725 (tttp) REVERT: H 62 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8070 (mmmm) outliers start: 10 outliers final: 4 residues processed: 96 average time/residue: 0.2756 time to fit residues: 33.4979 Evaluate side-chains 91 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089578 restraints weight = 7567.106| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.54 r_work: 0.2887 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5758 Z= 0.109 Angle : 1.071 32.648 7895 Z= 0.396 Chirality : 0.115 2.127 912 Planarity : 0.004 0.041 898 Dihedral : 17.494 179.350 1501 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.07 % Allowed : 13.95 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.34), residues: 648 helix: 1.60 (0.30), residues: 329 sheet: -1.31 (0.47), residues: 111 loop : -1.26 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.004 0.001 HIS A 53 PHE 0.009 0.001 PHE A 340 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02612 ( 289) hydrogen bonds : angle 3.84316 ( 834) metal coordination : bond 0.00359 ( 4) metal coordination : angle 1.38208 ( 3) SS BOND : bond 0.00503 ( 3) SS BOND : angle 1.28065 ( 6) covalent geometry : bond 0.00248 ( 5750) covalent geometry : angle 1.07046 ( 7886) Misc. bond : bond 0.00022 ( 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 99 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.574 Fit side-chains REVERT: A 112 MET cc_start: 0.8141 (ptp) cc_final: 0.7801 (ptt) REVERT: A 188 ARG cc_start: 0.7562 (mtt180) cc_final: 0.6915 (mmt-90) REVERT: A 191 GLN cc_start: 0.7944 (tt0) cc_final: 0.7594 (mt0) REVERT: A 235 ARG cc_start: 0.7311 (mmt180) cc_final: 0.5922 (mtm110) REVERT: A 375 ARG cc_start: 0.5708 (mmt180) cc_final: 0.5315 (mmt180) REVERT: A 386 LEU cc_start: 0.9115 (pt) cc_final: 0.8728 (mp) REVERT: A 436 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8057 (tt0) REVERT: A 453 ARG cc_start: 0.7710 (ttt90) cc_final: 0.7017 (ttp-170) REVERT: L 98 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7044 (mp) REVERT: H 38 LYS cc_start: 0.8807 (tttt) cc_final: 0.8483 (tttp) REVERT: H 62 LYS cc_start: 0.8315 (mmtm) cc_final: 0.7726 (mmmm) REVERT: H 127 TYR cc_start: 0.8771 (m-80) cc_final: 0.8225 (m-80) outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 0.2186 time to fit residues: 26.3921 Evaluate side-chains 93 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 98 LEU 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 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.0070 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.119399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.090237 restraints weight = 7549.587| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.54 r_work: 0.2995 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2200 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= 0.104 Angle : 1.065 32.615 7895 Z= 0.392 Chirality : 0.115 2.119 912 Planarity : 0.004 0.040 898 Dihedral : 17.423 179.609 1501 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.43 % Allowed : 15.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.34), residues: 648 helix: 1.80 (0.29), residues: 331 sheet: -1.20 (0.48), residues: 111 loop : -1.17 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 PHE 0.009 0.001 PHE A 340 TYR 0.020 0.001 TYR A 452 ARG 0.002 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02515 ( 289) hydrogen bonds : angle 3.75475 ( 834) metal coordination : bond 0.00299 ( 4) metal coordination : angle 1.34326 ( 3) SS BOND : bond 0.00323 ( 3) SS BOND : angle 1.21749 ( 6) covalent geometry : bond 0.00236 ( 5750) covalent geometry : angle 1.06437 ( 7886) Misc. bond : bond 0.00018 ( 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 104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.618 Fit side-chains REVERT: A 112 MET cc_start: 0.8190 (ptp) cc_final: 0.7839 (ptt) REVERT: A 132 MET cc_start: 0.8092 (mtp) cc_final: 0.7807 (mtm) REVERT: A 188 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7058 (mmt-90) REVERT: A 191 GLN cc_start: 0.7974 (tt0) cc_final: 0.7627 (mt0) REVERT: A 235 ARG cc_start: 0.7256 (mmt180) cc_final: 0.5989 (mtm110) REVERT: A 375 ARG cc_start: 0.5654 (mmt180) cc_final: 0.5353 (mmt180) REVERT: A 386 LEU cc_start: 0.9133 (pt) cc_final: 0.8774 (mp) REVERT: A 436 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8097 (tt0) REVERT: A 453 ARG cc_start: 0.7696 (ttt90) cc_final: 0.7086 (ttp-170) REVERT: L 81 ARG cc_start: 0.8493 (ptt-90) cc_final: 0.8254 (ptt-90) REVERT: L 98 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7231 (mp) REVERT: H 38 LYS cc_start: 0.8920 (tttt) cc_final: 0.8625 (tttp) REVERT: H 62 LYS cc_start: 0.8492 (mmtm) cc_final: 0.7909 (mmmm) REVERT: H 127 TYR cc_start: 0.8849 (m-80) cc_final: 0.8334 (m-80) outliers start: 8 outliers final: 3 residues processed: 100 average time/residue: 0.2114 time to fit residues: 26.5526 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 : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.0270 chunk 63 optimal weight: 0.0570 chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 8 optimal weight: 1.9990 overall best weight: 0.2854 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.122877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.093838 restraints weight = 7512.969| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.56 r_work: 0.2948 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2520 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= 0.085 Angle : 1.054 32.387 7895 Z= 0.386 Chirality : 0.114 2.094 912 Planarity : 0.004 0.038 898 Dihedral : 17.374 179.446 1501 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.89 % Allowed : 16.64 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.35), residues: 648 helix: 2.03 (0.30), residues: 331 sheet: -0.83 (0.52), residues: 103 loop : -1.09 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 120 HIS 0.004 0.000 HIS A 53 PHE 0.007 0.001 PHE A 340 TYR 0.017 0.001 TYR A 452 ARG 0.002 0.000 ARG L 81 Details of bonding type rmsd hydrogen bonds : bond 0.02280 ( 289) hydrogen bonds : angle 3.62156 ( 834) metal coordination : bond 0.00244 ( 4) metal coordination : angle 1.20707 ( 3) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.82797 ( 6) covalent geometry : bond 0.00180 ( 5750) covalent geometry : angle 1.05385 ( 7886) Misc. bond : bond 0.00008 ( 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 104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.600 Fit side-chains REVERT: A 109 MET cc_start: 0.7055 (tmm) cc_final: 0.6631 (tmm) REVERT: A 112 MET cc_start: 0.8073 (ptp) cc_final: 0.7756 (ptt) REVERT: A 132 MET cc_start: 0.7779 (mtp) cc_final: 0.7564 (mtm) REVERT: A 191 GLN cc_start: 0.7774 (tt0) cc_final: 0.7437 (mt0) REVERT: A 235 ARG cc_start: 0.7195 (mmt180) cc_final: 0.5957 (mtm110) REVERT: A 362 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7462 (tpp80) REVERT: A 386 LEU cc_start: 0.9166 (pt) cc_final: 0.8804 (mp) REVERT: A 427 MET cc_start: 0.7210 (ttp) cc_final: 0.6930 (tmm) REVERT: A 436 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7999 (tt0) REVERT: A 452 TYR cc_start: 0.8284 (t80) cc_final: 0.7908 (t80) REVERT: A 453 ARG cc_start: 0.7593 (ttt90) cc_final: 0.6864 (ttp-170) REVERT: L 81 ARG cc_start: 0.8333 (ptt-90) cc_final: 0.8129 (ptt-90) REVERT: L 98 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7134 (mp) REVERT: H 38 LYS cc_start: 0.8794 (tttt) cc_final: 0.8497 (tttp) REVERT: H 62 LYS cc_start: 0.8379 (mmtm) cc_final: 0.7760 (mmmm) REVERT: H 127 TYR cc_start: 0.8698 (m-80) cc_final: 0.8077 (m-80) outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 0.2233 time to fit residues: 28.6518 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 : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Chi-restraints excluded: chain L residue 98 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 50 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 0.0270 chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.118336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091003 restraints weight = 7436.937| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.39 r_work: 0.2911 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5758 Z= 0.112 Angle : 1.067 32.662 7895 Z= 0.394 Chirality : 0.115 2.116 912 Planarity : 0.004 0.038 898 Dihedral : 17.345 179.834 1501 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.07 % Allowed : 16.46 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.35), residues: 648 helix: 2.07 (0.30), residues: 330 sheet: -0.89 (0.50), residues: 111 loop : -0.99 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 PHE 0.008 0.001 PHE A 167 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG L 81 Details of bonding type rmsd hydrogen bonds : bond 0.02556 ( 289) hydrogen bonds : angle 3.67562 ( 834) metal coordination : bond 0.00335 ( 4) metal coordination : angle 1.43435 ( 3) SS BOND : bond 0.00359 ( 3) SS BOND : angle 1.16769 ( 6) covalent geometry : bond 0.00257 ( 5750) covalent geometry : angle 1.06683 ( 7886) Misc. bond : bond 0.00013 ( 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 100 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.653 Fit side-chains REVERT: A 109 MET cc_start: 0.7190 (tmm) cc_final: 0.6754 (tmm) REVERT: A 112 MET cc_start: 0.8205 (ptp) cc_final: 0.7856 (ptt) REVERT: A 128 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8051 (ttp) REVERT: A 132 MET cc_start: 0.8250 (mtp) cc_final: 0.7881 (mtm) REVERT: A 191 GLN cc_start: 0.7927 (tt0) cc_final: 0.7578 (mt0) REVERT: A 235 ARG cc_start: 0.7362 (mmt180) cc_final: 0.5857 (mtm110) REVERT: A 375 ARG cc_start: 0.5670 (mmt180) cc_final: 0.5198 (mmt90) REVERT: A 427 MET cc_start: 0.7297 (ttp) cc_final: 0.7007 (tmm) REVERT: A 436 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8081 (tt0) REVERT: A 452 TYR cc_start: 0.8358 (t80) cc_final: 0.8007 (t80) REVERT: A 453 ARG cc_start: 0.7606 (ttt90) cc_final: 0.6867 (ttp-170) REVERT: L 81 ARG cc_start: 0.8354 (ptt-90) cc_final: 0.8105 (ptt-90) REVERT: L 98 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7070 (mp) REVERT: H 38 LYS cc_start: 0.8807 (tttt) cc_final: 0.8506 (tttp) REVERT: H 62 LYS cc_start: 0.8380 (mmtm) cc_final: 0.7765 (mmmm) REVERT: H 127 TYR cc_start: 0.8813 (m-80) cc_final: 0.8217 (m-80) outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.2042 time to fit residues: 25.3374 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 : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091273 restraints weight = 7559.709| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.58 r_work: 0.2911 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2556 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= 0.102 Angle : 1.063 32.535 7895 Z= 0.391 Chirality : 0.115 2.113 912 Planarity : 0.004 0.038 898 Dihedral : 17.321 179.718 1501 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.61 % Allowed : 16.28 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.35), residues: 648 helix: 2.10 (0.30), residues: 332 sheet: -0.58 (0.53), residues: 101 loop : -1.09 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 PHE 0.008 0.001 PHE A 340 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02487 ( 289) hydrogen bonds : angle 3.65128 ( 834) metal coordination : bond 0.00277 ( 4) metal coordination : angle 1.31503 ( 3) SS BOND : bond 0.00314 ( 3) SS BOND : angle 1.02836 ( 6) covalent geometry : bond 0.00231 ( 5750) covalent geometry : angle 1.06249 ( 7886) Misc. bond : bond 0.00011 ( 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 101 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.7091 (tmm) cc_final: 0.6648 (tmm) REVERT: A 112 MET cc_start: 0.8131 (ptp) cc_final: 0.7744 (ptt) REVERT: A 128 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8015 (ttp) REVERT: A 132 MET cc_start: 0.7939 (mtp) cc_final: 0.7631 (mtm) REVERT: A 191 GLN cc_start: 0.7832 (tt0) cc_final: 0.7514 (mt0) REVERT: A 235 ARG cc_start: 0.7306 (mmt180) cc_final: 0.5925 (mtm110) REVERT: A 375 ARG cc_start: 0.5724 (mmt180) cc_final: 0.5265 (mmt90) REVERT: A 427 MET cc_start: 0.7302 (ttp) cc_final: 0.7032 (tmm) REVERT: A 452 TYR cc_start: 0.8366 (t80) cc_final: 0.8003 (t80) REVERT: A 453 ARG cc_start: 0.7505 (ttt90) cc_final: 0.6825 (ttp-170) REVERT: L 98 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7141 (mp) REVERT: H 38 LYS cc_start: 0.8815 (tttt) cc_final: 0.8500 (tttp) REVERT: H 62 LYS cc_start: 0.8394 (mmtm) cc_final: 0.7784 (mmmm) REVERT: H 127 TYR cc_start: 0.8770 (m-80) cc_final: 0.8190 (m-80) outliers start: 9 outliers final: 4 residues processed: 98 average time/residue: 0.2044 time to fit residues: 25.6277 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 : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET 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 15 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 43 optimal weight: 7.9990 chunk 22 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.121677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.092420 restraints weight = 7537.190| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.59 r_work: 0.2926 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5758 Z= 0.098 Angle : 1.064 32.491 7895 Z= 0.393 Chirality : 0.115 2.109 912 Planarity : 0.004 0.038 898 Dihedral : 17.312 179.703 1501 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.89 % Allowed : 16.64 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.35), residues: 648 helix: 2.17 (0.30), residues: 332 sheet: -0.53 (0.53), residues: 101 loop : -1.07 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 120 HIS 0.003 0.000 HIS A 53 PHE 0.008 0.001 PHE A 340 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02404 ( 289) hydrogen bonds : angle 3.61998 ( 834) metal coordination : bond 0.00256 ( 4) metal coordination : angle 1.33536 ( 3) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.98134 ( 6) covalent geometry : bond 0.00219 ( 5750) covalent geometry : angle 1.06419 ( 7886) Misc. bond : bond 0.00007 ( 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 98 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.604 Fit side-chains REVERT: A 109 MET cc_start: 0.7144 (tmm) cc_final: 0.6699 (tmm) REVERT: A 112 MET cc_start: 0.8076 (ptp) cc_final: 0.7724 (ptt) REVERT: A 128 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8014 (ttp) REVERT: A 132 MET cc_start: 0.7903 (mtp) cc_final: 0.7617 (mtm) REVERT: A 191 GLN cc_start: 0.7813 (tt0) cc_final: 0.7505 (mt0) REVERT: A 235 ARG cc_start: 0.7286 (mmt180) cc_final: 0.6772 (ptt-90) REVERT: A 375 ARG cc_start: 0.5612 (mmt180) cc_final: 0.5187 (mmt90) REVERT: A 427 MET cc_start: 0.7318 (ttp) cc_final: 0.7072 (tmm) REVERT: A 452 TYR cc_start: 0.8351 (t80) cc_final: 0.8005 (t80) REVERT: A 453 ARG cc_start: 0.7505 (ttt90) cc_final: 0.6780 (ttp-170) REVERT: L 98 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7142 (mp) REVERT: H 38 LYS cc_start: 0.8810 (tttt) cc_final: 0.8503 (tttp) REVERT: H 62 LYS cc_start: 0.8428 (mmtm) cc_final: 0.7825 (mmmm) REVERT: H 127 TYR cc_start: 0.8745 (m-80) cc_final: 0.8167 (m-80) outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.2016 time to fit residues: 24.7711 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 : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain L residue 21 ASP 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 24 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 13 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.121770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092528 restraints weight = 7612.209| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.57 r_work: 0.2929 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5758 Z= 0.099 Angle : 1.064 32.506 7895 Z= 0.393 Chirality : 0.115 2.108 912 Planarity : 0.004 0.039 898 Dihedral : 17.305 179.764 1501 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.07 % Allowed : 16.82 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.35), residues: 648 helix: 2.20 (0.30), residues: 332 sheet: -0.50 (0.54), residues: 101 loop : -1.04 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 PHE 0.008 0.001 PHE A 340 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.02410 ( 289) hydrogen bonds : angle 3.63133 ( 834) metal coordination : bond 0.00270 ( 4) metal coordination : angle 1.36528 ( 3) SS BOND : bond 0.00280 ( 3) SS BOND : angle 1.08102 ( 6) covalent geometry : bond 0.00224 ( 5750) covalent geometry : angle 1.06396 ( 7886) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3953.17 seconds wall clock time: 70 minutes 51.51 seconds (4251.51 seconds total)