Starting phenix.real_space_refine on Tue Feb 11 14:58:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7urc_26708/02_2025/7urc_26708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urc_26708/02_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_26708/02_2025/7urc_26708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urc_26708/02_2025/7urc_26708.map" model { file = "/net/cci-nas-00/data/ceres_data/7urc_26708/02_2025/7urc_26708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urc_26708/02_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-5592/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: 4.18, per 1000 atoms: 0.75 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: 1.59 Conformation dependent library (CDL) restraints added in 918.7 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: 0.64 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: 1.72 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: 0.010 Normalize map: mean=0, sd=1: 1.120 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- 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 : 0.018 0.428 5750 Z= 0.899 Angle : 1.001 12.444 7886 Z= 0.407 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 *********************** 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 : 0.547 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: 0.2304 time to fit residues: 32.2446 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 : 0.555 ------------------------------------------------------------------------------- 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 = 0.113881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.085685 restraints weight = 7626.542| |-----------------------------------------------------------------------------| 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: 0.2752 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 5750 Z= 0.284 Angle : 1.156 33.536 7886 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 *********************** 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 : 0.549 Fit side-chains REVERT: A 112 MET cc_start: 0.8278 (ptp) cc_final: 0.7838 (ptt) REVERT: A 188 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7160 (mtp85) REVERT: A 191 GLN cc_start: 0.8080 (tt0) cc_final: 0.7707 (mt0) REVERT: A 235 ARG cc_start: 0.7309 (mmt180) cc_final: 0.6701 (ptt-90) REVERT: A 386 LEU cc_start: 0.8979 (pt) cc_final: 0.8554 (mp) REVERT: A 453 ARG cc_start: 0.7982 (ttt90) cc_final: 0.7210 (ttt180) REVERT: L 56 TYR cc_start: 0.9396 (m-80) cc_final: 0.9115 (m-80) REVERT: L 72 LYS cc_start: 0.9065 (ptpt) cc_final: 0.8651 (ptmm) REVERT: L 81 ARG cc_start: 0.8585 (ptt-90) cc_final: 0.8131 (ptt-90) REVERT: L 98 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7259 (mp) REVERT: H 38 LYS cc_start: 0.8990 (tttt) cc_final: 0.8653 (tttp) REVERT: H 62 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8077 (mmmm) outliers start: 7 outliers final: 2 residues processed: 93 average time/residue: 0.2279 time to fit residues: 26.2472 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 : 0.593 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.118133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088890 restraints weight = 7561.344| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.57 r_work: 0.2922 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5750 Z= 0.172 Angle : 1.086 32.385 7886 Z= 0.403 Chirality : 0.116 2.168 912 Planarity : 0.004 0.044 898 Dihedral : 17.748 179.900 1501 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.43 % Allowed : 11.63 % Favored : 86.94 % 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: -0.41 (0.34), residues: 648 helix: 1.13 (0.30), residues: 329 sheet: -1.72 (0.44), residues: 110 loop : -1.65 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 300 HIS 0.005 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 *********************** 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 102 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.572 Fit side-chains REVERT: A 112 MET cc_start: 0.8093 (ptp) cc_final: 0.7738 (ptt) REVERT: A 132 MET cc_start: 0.8387 (mtp) cc_final: 0.8126 (mtp) REVERT: A 188 ARG cc_start: 0.7543 (mtt180) cc_final: 0.7086 (mtp85) REVERT: A 191 GLN cc_start: 0.7956 (tt0) cc_final: 0.7589 (mt0) REVERT: A 235 ARG cc_start: 0.7172 (mmt180) cc_final: 0.6519 (ptt-90) REVERT: A 386 LEU cc_start: 0.9013 (pt) cc_final: 0.8612 (mp) REVERT: A 436 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8160 (tt0) REVERT: A 453 ARG cc_start: 0.7840 (ttt90) cc_final: 0.7186 (ttp-170) REVERT: L 81 ARG cc_start: 0.8503 (ptt-90) cc_final: 0.8095 (ptt-90) REVERT: H 38 LYS cc_start: 0.8961 (tttt) cc_final: 0.8657 (tttp) REVERT: H 62 LYS cc_start: 0.8494 (mmtm) cc_final: 0.7971 (mmmm) REVERT: H 127 TYR cc_start: 0.8822 (m-80) cc_final: 0.8316 (m-80) outliers start: 8 outliers final: 2 residues processed: 99 average time/residue: 0.2314 time to fit residues: 28.2795 Evaluate side-chains 95 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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: 0.8980 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.117556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.088288 restraints weight = 7744.181| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.59 r_work: 0.2903 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5750 Z= 0.193 Angle : 1.081 32.978 7886 Z= 0.403 Chirality : 0.116 2.163 912 Planarity : 0.004 0.043 898 Dihedral : 17.583 179.076 1501 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.43 % Allowed : 12.88 % 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 (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: -0.01 (0.34), residues: 648 helix: 1.42 (0.30), residues: 329 sheet: -1.52 (0.46), residues: 111 loop : -1.39 (0.42), 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 167 TYR 0.020 0.001 TYR A 452 ARG 0.003 0.000 ARG A 6 *********************** 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: 8 poor density : 90 time to evaluate : 0.509 Fit side-chains REVERT: A 112 MET cc_start: 0.8224 (ptp) cc_final: 0.7863 (ptt) REVERT: A 188 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7239 (mtp85) REVERT: A 191 GLN cc_start: 0.8087 (tt0) cc_final: 0.7707 (mt0) REVERT: A 235 ARG cc_start: 0.7254 (mmt180) cc_final: 0.6566 (ptt-90) REVERT: A 386 LEU cc_start: 0.9118 (pt) cc_final: 0.8736 (mp) REVERT: A 436 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8163 (tt0) REVERT: A 453 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7221 (ttp-170) REVERT: H 38 LYS cc_start: 0.8997 (tttt) cc_final: 0.8723 (tttp) REVERT: H 62 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8003 (mmmm) REVERT: H 127 TYR cc_start: 0.8894 (m-80) cc_final: 0.8457 (m-80) outliers start: 8 outliers final: 2 residues processed: 95 average time/residue: 0.2189 time to fit residues: 25.9515 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 : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain L residue 21 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN H 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.090391 restraints weight = 7546.725| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.54 r_work: 0.2896 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5750 Z= 0.148 Angle : 1.067 32.579 7886 Z= 0.393 Chirality : 0.115 2.120 912 Planarity : 0.004 0.040 898 Dihedral : 17.463 179.381 1501 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.89 % Allowed : 14.31 % Favored : 84.79 % 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: 0.32 (0.34), residues: 648 helix: 1.66 (0.30), residues: 330 sheet: -1.33 (0.47), residues: 111 loop : -1.21 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 120 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 6 *********************** 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 104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.522 Fit side-chains REVERT: A 112 MET cc_start: 0.8145 (ptp) cc_final: 0.7820 (ptt) REVERT: A 132 MET cc_start: 0.8118 (mtp) cc_final: 0.7844 (mtm) REVERT: A 188 ARG cc_start: 0.7552 (mtt180) cc_final: 0.6909 (mmt-90) REVERT: A 191 GLN cc_start: 0.7927 (tt0) cc_final: 0.7577 (mt0) REVERT: A 235 ARG cc_start: 0.7295 (mmt180) cc_final: 0.5896 (mtm110) REVERT: A 375 ARG cc_start: 0.5691 (mmt180) cc_final: 0.5348 (mmt180) REVERT: A 386 LEU cc_start: 0.9114 (pt) cc_final: 0.8729 (mp) REVERT: A 436 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8051 (tt0) REVERT: A 453 ARG cc_start: 0.7722 (ttt90) cc_final: 0.7029 (ttp-170) REVERT: H 38 LYS cc_start: 0.8802 (tttt) cc_final: 0.8484 (tttp) REVERT: H 62 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7707 (mmmm) REVERT: H 127 TYR cc_start: 0.8762 (m-80) cc_final: 0.8213 (m-80) outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 0.2183 time to fit residues: 28.0133 Evaluate side-chains 94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.119841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.090559 restraints weight = 7527.756| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.54 r_work: 0.2900 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5750 Z= 0.149 Angle : 1.064 32.590 7886 Z= 0.392 Chirality : 0.115 2.118 912 Planarity : 0.004 0.040 898 Dihedral : 17.411 179.533 1501 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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 (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: 0.53 (0.34), residues: 648 helix: 1.81 (0.30), residues: 331 sheet: -1.18 (0.48), residues: 111 loop : -1.13 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 6 *********************** 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 98 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.608 Fit side-chains REVERT: A 112 MET cc_start: 0.8189 (ptp) cc_final: 0.7858 (ptt) REVERT: A 132 MET cc_start: 0.8212 (mtp) cc_final: 0.7905 (mtm) REVERT: A 188 ARG cc_start: 0.7606 (mtt180) cc_final: 0.6982 (mmt-90) REVERT: A 191 GLN cc_start: 0.7969 (tt0) cc_final: 0.7611 (mt0) REVERT: A 235 ARG cc_start: 0.7304 (mmt180) cc_final: 0.5930 (mtm110) REVERT: A 386 LEU cc_start: 0.9123 (pt) cc_final: 0.8752 (mp) REVERT: A 436 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8106 (tt0) REVERT: A 453 ARG cc_start: 0.7696 (ttt90) cc_final: 0.6989 (ttp-170) REVERT: L 81 ARG cc_start: 0.8362 (ptt-90) cc_final: 0.8053 (ptt-90) REVERT: H 38 LYS cc_start: 0.8840 (tttt) cc_final: 0.8530 (tttp) REVERT: H 62 LYS cc_start: 0.8374 (mmtm) cc_final: 0.7768 (mmmm) REVERT: H 127 TYR cc_start: 0.8803 (m-80) cc_final: 0.8269 (m-80) outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.2165 time to fit residues: 26.6529 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 : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP 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: 0.8980 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.118247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.088989 restraints weight = 7580.480| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.57 r_work: 0.2922 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5750 Z= 0.180 Angle : 1.069 32.704 7886 Z= 0.395 Chirality : 0.115 2.128 912 Planarity : 0.004 0.039 898 Dihedral : 17.383 179.789 1501 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.89 % Allowed : 16.28 % Favored : 82.83 % 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: 0.65 (0.35), residues: 648 helix: 1.89 (0.29), residues: 331 sheet: -1.09 (0.49), residues: 111 loop : -1.06 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 PHE 0.009 0.001 PHE A 167 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 183 *********************** 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 96 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.596 Fit side-chains REVERT: A 112 MET cc_start: 0.8186 (ptp) cc_final: 0.7840 (ptt) REVERT: A 132 MET cc_start: 0.8151 (mtp) cc_final: 0.7853 (mtp) REVERT: A 191 GLN cc_start: 0.7950 (tt0) cc_final: 0.7606 (mt0) REVERT: A 235 ARG cc_start: 0.7250 (mmt180) cc_final: 0.5903 (mtm110) REVERT: A 375 ARG cc_start: 0.5632 (mmt180) cc_final: 0.5103 (mmt90) REVERT: A 427 MET cc_start: 0.7401 (ttp) cc_final: 0.7061 (tmm) REVERT: A 436 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8080 (tt0) REVERT: A 452 TYR cc_start: 0.8395 (t80) cc_final: 0.8096 (t80) REVERT: A 453 ARG cc_start: 0.7662 (ttt90) cc_final: 0.6997 (ttp-170) REVERT: L 81 ARG cc_start: 0.8446 (ptt-90) cc_final: 0.8207 (ptt-90) REVERT: L 98 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7184 (mp) REVERT: H 38 LYS cc_start: 0.8886 (tttt) cc_final: 0.8622 (tttp) REVERT: H 62 LYS cc_start: 0.8466 (mmtm) cc_final: 0.7861 (mmmm) REVERT: H 127 TYR cc_start: 0.8837 (m-80) cc_final: 0.8302 (m-80) outliers start: 5 outliers final: 3 residues processed: 94 average time/residue: 0.2237 time to fit residues: 26.4408 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 : 0.600 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 53 optimal weight: 0.0470 chunk 15 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.118407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.091233 restraints weight = 7422.204| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.39 r_work: 0.3018 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5750 Z= 0.142 Angle : 1.059 32.501 7886 Z= 0.389 Chirality : 0.115 2.114 912 Planarity : 0.004 0.039 898 Dihedral : 17.350 179.629 1501 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.89 % Allowed : 16.46 % Favored : 82.65 % 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: 0.86 (0.35), residues: 648 helix: 2.06 (0.30), residues: 331 sheet: -0.93 (0.50), residues: 111 loop : -1.01 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 L 81 *********************** 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 95 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.665 Fit side-chains REVERT: A 109 MET cc_start: 0.7255 (tmm) cc_final: 0.6825 (tmm) REVERT: A 112 MET cc_start: 0.8209 (ptp) cc_final: 0.7873 (ptt) REVERT: A 132 MET cc_start: 0.8202 (mtp) cc_final: 0.7906 (mtm) REVERT: A 191 GLN cc_start: 0.8035 (tt0) cc_final: 0.7676 (mt0) REVERT: A 235 ARG cc_start: 0.7350 (mmt180) cc_final: 0.5944 (mtm110) REVERT: A 375 ARG cc_start: 0.5842 (mmt180) cc_final: 0.5355 (mmt90) REVERT: A 427 MET cc_start: 0.7446 (ttp) cc_final: 0.7128 (tmm) REVERT: A 436 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8168 (tt0) REVERT: A 452 TYR cc_start: 0.8446 (t80) cc_final: 0.8074 (t80) REVERT: A 453 ARG cc_start: 0.7683 (ttt90) cc_final: 0.6931 (ttp-170) REVERT: H 38 LYS cc_start: 0.8896 (tttt) cc_final: 0.8596 (tttp) REVERT: H 62 LYS cc_start: 0.8508 (mmtm) cc_final: 0.7895 (mmmm) REVERT: H 127 TYR cc_start: 0.8877 (m-80) cc_final: 0.8360 (m-80) outliers start: 5 outliers final: 4 residues processed: 94 average time/residue: 0.2254 time to fit residues: 26.8608 Evaluate side-chains 90 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090821 restraints weight = 7562.286| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.54 r_work: 0.3001 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5750 Z= 0.163 Angle : 1.063 32.614 7886 Z= 0.392 Chirality : 0.115 2.119 912 Planarity : 0.004 0.039 898 Dihedral : 17.342 179.800 1501 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.07 % Allowed : 15.92 % 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 (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: 0.91 (0.35), residues: 648 helix: 2.12 (0.30), residues: 330 sheet: -0.88 (0.50), residues: 111 loop : -1.02 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 120 HIS 0.003 0.001 HIS A 53 PHE 0.008 0.001 PHE A 340 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 183 *********************** 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 95 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.601 Fit side-chains REVERT: A 109 MET cc_start: 0.7179 (tmm) cc_final: 0.6731 (tmm) REVERT: A 112 MET cc_start: 0.8215 (ptp) cc_final: 0.7829 (ptt) REVERT: A 128 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8148 (ttp) REVERT: A 132 MET cc_start: 0.8113 (mtp) cc_final: 0.7777 (mtm) REVERT: A 191 GLN cc_start: 0.7978 (tt0) cc_final: 0.7631 (mt0) REVERT: A 235 ARG cc_start: 0.7235 (mmt180) cc_final: 0.5901 (mtm110) REVERT: A 375 ARG cc_start: 0.5751 (mmt180) cc_final: 0.5266 (mmt90) REVERT: A 427 MET cc_start: 0.7388 (ttp) cc_final: 0.7097 (tmm) REVERT: A 436 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8126 (tt0) REVERT: A 452 TYR cc_start: 0.8474 (t80) cc_final: 0.8128 (t80) REVERT: A 453 ARG cc_start: 0.7623 (ttt90) cc_final: 0.6939 (ttp-170) REVERT: L 98 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7257 (mp) REVERT: H 38 LYS cc_start: 0.8912 (tttt) cc_final: 0.8632 (tttp) REVERT: H 62 LYS cc_start: 0.8539 (mmtm) cc_final: 0.7939 (mmmm) REVERT: H 127 TYR cc_start: 0.8852 (m-80) cc_final: 0.8343 (m-80) outliers start: 6 outliers final: 4 residues processed: 93 average time/residue: 0.2020 time to fit residues: 24.0013 Evaluate side-chains 94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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: 0.8980 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.119037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089802 restraints weight = 7600.830| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.55 r_work: 0.2988 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5750 Z= 0.177 Angle : 1.065 32.661 7886 Z= 0.394 Chirality : 0.115 2.129 912 Planarity : 0.004 0.039 898 Dihedral : 17.336 179.867 1501 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.07 % Allowed : 15.92 % 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 (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: 0.93 (0.35), residues: 648 helix: 2.14 (0.30), residues: 330 sheet: -0.88 (0.50), residues: 111 loop : -1.00 (0.44), residues: 207 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 0.009 0.001 PHE A 167 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 183 ********************** 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 96 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.620 Fit side-chains REVERT: A 109 MET cc_start: 0.7154 (tmm) cc_final: 0.6718 (tmm) REVERT: A 112 MET cc_start: 0.8171 (ptp) cc_final: 0.7816 (ptt) REVERT: A 128 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8145 (ttp) REVERT: A 132 MET cc_start: 0.8174 (mtp) cc_final: 0.7814 (mtm) REVERT: A 191 GLN cc_start: 0.7994 (tt0) cc_final: 0.7645 (mt0) REVERT: A 235 ARG cc_start: 0.7233 (mmt180) cc_final: 0.5867 (mtm110) REVERT: A 375 ARG cc_start: 0.5656 (mmt180) cc_final: 0.5189 (mmt90) REVERT: A 427 MET cc_start: 0.7387 (ttp) cc_final: 0.7095 (tmm) REVERT: A 436 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8104 (tt0) REVERT: A 452 TYR cc_start: 0.8479 (t80) cc_final: 0.8127 (t80) REVERT: A 453 ARG cc_start: 0.7596 (ttt90) cc_final: 0.6934 (ttp-170) REVERT: L 98 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7265 (mp) REVERT: H 38 LYS cc_start: 0.8909 (tttt) cc_final: 0.8654 (tttp) REVERT: H 62 LYS cc_start: 0.8527 (mmtm) cc_final: 0.7931 (mmmm) REVERT: H 127 TYR cc_start: 0.8855 (m-80) cc_final: 0.8414 (m-80) outliers start: 6 outliers final: 4 residues processed: 94 average time/residue: 0.2052 time to fit residues: 24.7259 Evaluate side-chains 95 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.085925 restraints weight = 7737.195| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.58 r_work: 0.2925 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5750 Z= 0.294 Angle : 1.097 33.157 7886 Z= 0.413 Chirality : 0.116 2.170 912 Planarity : 0.004 0.042 898 Dihedral : 17.405 179.893 1501 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.25 % Allowed : 16.28 % 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: 0.77 (0.35), residues: 648 helix: 1.92 (0.29), residues: 330 sheet: -0.93 (0.50), residues: 112 loop : -0.92 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 120 HIS 0.002 0.001 HIS A 341 PHE 0.011 0.001 PHE A 167 TYR 0.020 0.002 TYR A 83 ARG 0.002 0.000 ARG A 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.82 seconds wall clock time: 50 minutes 5.79 seconds (3005.79 seconds total)