Starting phenix.real_space_refine on Wed Jul 23 10:28:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymj_33930/07_2025/7ymj_33930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymj_33930/07_2025/7ymj_33930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ymj_33930/07_2025/7ymj_33930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymj_33930/07_2025/7ymj_33930.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymj_33930/07_2025/7ymj_33930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymj_33930/07_2025/7ymj_33930.cif" } resolution = 3.35 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= -0.002 sd= 0.170 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2022 2.51 5 N 511 2.21 5 O 532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3085 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2215 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 265} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 842 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'JGX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.72, per 1000 atoms: 0.88 Number of scatterers: 3085 At special positions: 0 Unit cell: (63.64, 63.64, 127.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 532 8.00 N 511 7.00 C 2022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 352.2 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 59.6% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 25 through 54 removed outlier: 3.820A pdb=" N LEU A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 79 removed outlier: 3.713A pdb=" N ILE A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.578A pdb=" N SER A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 130 removed outlier: 3.651A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 103 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.688A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 159 removed outlier: 3.599A pdb=" N GLY A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.853A pdb=" N PHE A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 214 removed outlier: 3.590A pdb=" N LEU A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 298 removed outlier: 4.544A pdb=" N ARG A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.060A pdb=" N VAL A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 312' Processing helix chain 'A' and resid 313 through 322 removed outlier: 3.986A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.763A pdb=" N CYS A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 343 removed outlier: 3.876A pdb=" N LYS A 335 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.856A pdb=" N SER D 72 " --> pdb=" O TYR D 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.999A pdb=" N GLY D 12 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 119 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 93 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D 98 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY D 37 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP D 35 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG D 102 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU D 33 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET D 36 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 53 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 52 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.999A pdb=" N GLY D 12 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 119 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 93 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 99 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 101 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 110 " --> pdb=" O TYR D 101 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 946 1.35 - 1.47: 830 1.47 - 1.59: 1356 1.59 - 1.71: 1 1.71 - 1.83: 26 Bond restraints: 3159 Sorted by residual: bond pdb=" C19 JGX A 401 " pdb=" O26 JGX A 401 " ideal model delta sigma weight residual 1.338 1.399 -0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" C9 JGX A 401 " pdb=" O10 JGX A 401 " ideal model delta sigma weight residual 1.347 1.406 -0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" N25 JGX A 401 " pdb=" S22 JGX A 401 " ideal model delta sigma weight residual 1.653 1.706 -0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C4 JGX A 401 " pdb=" O3 JGX A 401 " ideal model delta sigma weight residual 1.346 1.398 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C20 JGX A 401 " pdb=" S22 JGX A 401 " ideal model delta sigma weight residual 1.771 1.821 -0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 3154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 4257 3.65 - 7.30: 42 7.30 - 10.95: 4 10.95 - 14.60: 1 14.60 - 18.25: 1 Bond angle restraints: 4305 Sorted by residual: angle pdb=" O23 JGX A 401 " pdb=" S22 JGX A 401 " pdb=" O24 JGX A 401 " ideal model delta sigma weight residual 118.38 100.13 18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 109.81 117.45 -7.64 2.21e+00 2.05e-01 1.20e+01 angle pdb=" N LEU A 286 " pdb=" CA LEU A 286 " pdb=" C LEU A 286 " ideal model delta sigma weight residual 109.81 117.44 -7.63 2.21e+00 2.05e-01 1.19e+01 angle pdb=" N ASN A 322 " pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 113.16 117.88 -4.72 1.42e+00 4.96e-01 1.11e+01 angle pdb=" N TYR A 326 " pdb=" CA TYR A 326 " pdb=" C TYR A 326 " ideal model delta sigma weight residual 109.81 116.37 -6.56 2.21e+00 2.05e-01 8.82e+00 ... (remaining 4300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 1598 15.85 - 31.70: 177 31.70 - 47.54: 58 47.54 - 63.39: 7 63.39 - 79.24: 1 Dihedral angle restraints: 1841 sinusoidal: 702 harmonic: 1139 Sorted by residual: dihedral pdb=" CA ASP D 74 " pdb=" CB ASP D 74 " pdb=" CG ASP D 74 " pdb=" OD1 ASP D 74 " ideal model delta sinusoidal sigma weight residual -30.00 -84.82 54.82 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA GLU A 180 " pdb=" CB GLU A 180 " pdb=" CG GLU A 180 " pdb=" CD GLU A 180 " ideal model delta sinusoidal sigma weight residual 60.00 107.24 -47.24 3 1.50e+01 4.44e-03 8.46e+00 dihedral pdb=" N LEU A 283 " pdb=" CA LEU A 283 " pdb=" CB LEU A 283 " pdb=" CG LEU A 283 " ideal model delta sinusoidal sigma weight residual -60.00 -106.50 46.50 3 1.50e+01 4.44e-03 8.35e+00 ... (remaining 1838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 307 0.039 - 0.079: 137 0.079 - 0.118: 33 0.118 - 0.158: 20 0.158 - 0.197: 4 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB VAL A 214 " pdb=" CA VAL A 214 " pdb=" CG1 VAL A 214 " pdb=" CG2 VAL A 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CA GLU A 173 " pdb=" N GLU A 173 " pdb=" C GLU A 173 " pdb=" CB GLU A 173 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 498 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 80 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO A 81 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 167 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 168 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 326 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 327 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.030 5.00e-02 4.00e+02 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1043 2.86 - 3.37: 2488 3.37 - 3.88: 4463 3.88 - 4.39: 4698 4.39 - 4.90: 8915 Nonbonded interactions: 21607 Sorted by model distance: nonbonded pdb=" OG SER D 9 " pdb=" OG SER D 23 " model vdw 2.349 3.040 nonbonded pdb=" O SER A 218 " pdb=" OG SER A 218 " model vdw 2.371 3.040 nonbonded pdb=" O GLY A 40 " pdb=" ND2 ASN A 44 " model vdw 2.391 3.120 nonbonded pdb=" N ASP D 111 " pdb=" OD1 ASP D 111 " model vdw 2.495 3.120 nonbonded pdb=" OD2 ASP A 72 " pdb=" NH1 ARG A 113 " model vdw 2.501 3.120 ... (remaining 21602 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: 0.910 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3161 Z= 0.267 Angle : 0.953 18.250 4309 Z= 0.486 Chirality : 0.052 0.197 501 Planarity : 0.007 0.068 527 Dihedral : 14.746 79.241 1107 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.45 (0.34), residues: 390 helix: -1.37 (0.30), residues: 195 sheet: -0.56 (0.77), residues: 50 loop : -4.25 (0.34), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.001 HIS A 56 PHE 0.023 0.002 PHE A 312 TYR 0.015 0.002 TYR A 204 ARG 0.003 0.000 ARG D 32 Details of bonding type rmsd hydrogen bonds : bond 0.14349 ( 169) hydrogen bonds : angle 4.71334 ( 489) SS BOND : bond 0.00396 ( 2) SS BOND : angle 1.52072 ( 4) covalent geometry : bond 0.00520 ( 3159) covalent geometry : angle 0.95270 ( 4305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.323 Fit side-chains REVERT: A 106 ASP cc_start: 0.8781 (t0) cc_final: 0.8302 (t0) REVERT: A 321 ILE cc_start: 0.7323 (tt) cc_final: 0.6977 (tt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1306 time to fit residues: 6.7530 Evaluate side-chains 36 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.185606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125498 restraints weight = 3270.205| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.49 r_work: 0.3261 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3161 Z= 0.148 Angle : 0.584 7.599 4309 Z= 0.299 Chirality : 0.041 0.125 501 Planarity : 0.005 0.046 527 Dihedral : 4.840 25.450 456 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.48 % Allowed : 9.94 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.25 (0.42), residues: 390 helix: 0.64 (0.36), residues: 205 sheet: -0.14 (0.82), residues: 50 loop : -3.53 (0.42), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.001 0.001 HIS A 56 PHE 0.014 0.001 PHE A 312 TYR 0.014 0.001 TYR A 204 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.08126 ( 169) hydrogen bonds : angle 3.84678 ( 489) SS BOND : bond 0.00323 ( 2) SS BOND : angle 1.47489 ( 4) covalent geometry : bond 0.00313 ( 3159) covalent geometry : angle 0.58210 ( 4305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.303 Fit side-chains REVERT: A 106 ASP cc_start: 0.8860 (t0) cc_final: 0.8438 (t0) REVERT: A 321 ILE cc_start: 0.7247 (tt) cc_final: 0.6822 (tt) REVERT: D 50 VAL cc_start: 0.8448 (p) cc_final: 0.8217 (m) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.0967 time to fit residues: 5.8025 Evaluate side-chains 40 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain D residue 84 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.189700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134707 restraints weight = 3188.179| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.20 r_work: 0.3339 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3161 Z= 0.116 Angle : 0.540 7.783 4309 Z= 0.271 Chirality : 0.039 0.122 501 Planarity : 0.004 0.038 527 Dihedral : 3.732 20.185 456 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.17 % Allowed : 13.66 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.45), residues: 390 helix: 1.42 (0.38), residues: 206 sheet: 0.33 (0.84), residues: 50 loop : -3.23 (0.45), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.001 HIS A 56 PHE 0.016 0.001 PHE A 312 TYR 0.011 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.06145 ( 169) hydrogen bonds : angle 3.54324 ( 489) SS BOND : bond 0.00182 ( 2) SS BOND : angle 1.16995 ( 4) covalent geometry : bond 0.00229 ( 3159) covalent geometry : angle 0.53879 ( 4305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.307 Fit side-chains REVERT: A 106 ASP cc_start: 0.8695 (t0) cc_final: 0.8282 (t0) REVERT: A 163 PHE cc_start: 0.6408 (t80) cc_final: 0.5984 (m-10) REVERT: D 50 VAL cc_start: 0.8483 (p) cc_final: 0.8264 (m) outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 0.0919 time to fit residues: 5.0455 Evaluate side-chains 38 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain D residue 84 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.182575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121297 restraints weight = 3252.704| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.47 r_work: 0.3212 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3161 Z= 0.172 Angle : 0.591 6.572 4309 Z= 0.300 Chirality : 0.042 0.123 501 Planarity : 0.004 0.032 527 Dihedral : 3.911 22.699 456 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.73 % Allowed : 14.29 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.45), residues: 390 helix: 1.74 (0.38), residues: 200 sheet: 0.40 (0.85), residues: 50 loop : -3.24 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.001 0.001 HIS A 56 PHE 0.015 0.001 PHE A 312 TYR 0.018 0.001 TYR A 204 ARG 0.002 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.08745 ( 169) hydrogen bonds : angle 3.75222 ( 489) SS BOND : bond 0.00233 ( 2) SS BOND : angle 1.30762 ( 4) covalent geometry : bond 0.00392 ( 3159) covalent geometry : angle 0.58977 ( 4305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.344 Fit side-chains REVERT: A 106 ASP cc_start: 0.8973 (t0) cc_final: 0.8531 (t0) REVERT: A 163 PHE cc_start: 0.6362 (t80) cc_final: 0.5951 (m-10) REVERT: D 50 VAL cc_start: 0.8500 (p) cc_final: 0.8276 (m) outliers start: 12 outliers final: 8 residues processed: 42 average time/residue: 0.0955 time to fit residues: 5.6319 Evaluate side-chains 43 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0050 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.187696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127841 restraints weight = 3177.658| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.42 r_work: 0.3291 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3161 Z= 0.128 Angle : 0.532 6.191 4309 Z= 0.269 Chirality : 0.040 0.121 501 Planarity : 0.003 0.031 527 Dihedral : 3.686 21.558 456 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.42 % Allowed : 15.53 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.45), residues: 390 helix: 2.01 (0.38), residues: 200 sheet: 0.34 (0.83), residues: 52 loop : -3.05 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.017 0.001 PHE A 312 TYR 0.014 0.001 TYR A 204 ARG 0.001 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.06907 ( 169) hydrogen bonds : angle 3.54920 ( 489) SS BOND : bond 0.00232 ( 2) SS BOND : angle 1.20053 ( 4) covalent geometry : bond 0.00265 ( 3159) covalent geometry : angle 0.53056 ( 4305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.304 Fit side-chains REVERT: A 106 ASP cc_start: 0.8788 (t0) cc_final: 0.8353 (t0) REVERT: D 50 VAL cc_start: 0.8508 (p) cc_final: 0.8297 (m) outliers start: 11 outliers final: 8 residues processed: 39 average time/residue: 0.0990 time to fit residues: 5.4157 Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain D residue 84 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.188225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127884 restraints weight = 3270.286| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.46 r_work: 0.3296 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3161 Z= 0.125 Angle : 0.525 5.975 4309 Z= 0.266 Chirality : 0.040 0.120 501 Planarity : 0.003 0.030 527 Dihedral : 3.584 21.596 456 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.35 % Allowed : 15.53 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.46), residues: 390 helix: 2.21 (0.38), residues: 200 sheet: 0.52 (0.82), residues: 52 loop : -2.87 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.017 0.001 PHE A 312 TYR 0.014 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.06747 ( 169) hydrogen bonds : angle 3.48139 ( 489) SS BOND : bond 0.00174 ( 2) SS BOND : angle 1.08656 ( 4) covalent geometry : bond 0.00257 ( 3159) covalent geometry : angle 0.52406 ( 4305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.326 Fit side-chains REVERT: A 106 ASP cc_start: 0.8764 (t0) cc_final: 0.8334 (t0) REVERT: A 297 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7627 (t80) REVERT: D 50 VAL cc_start: 0.8509 (p) cc_final: 0.8304 (m) outliers start: 14 outliers final: 9 residues processed: 42 average time/residue: 0.0927 time to fit residues: 5.4862 Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.184267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122934 restraints weight = 3227.692| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.44 r_work: 0.3236 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3161 Z= 0.158 Angle : 0.572 6.325 4309 Z= 0.290 Chirality : 0.042 0.135 501 Planarity : 0.003 0.028 527 Dihedral : 3.742 22.519 456 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.42 % Allowed : 15.84 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.45), residues: 390 helix: 2.12 (0.38), residues: 200 sheet: 0.59 (0.82), residues: 52 loop : -2.79 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.016 0.001 PHE A 312 TYR 0.016 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.08315 ( 169) hydrogen bonds : angle 3.65102 ( 489) SS BOND : bond 0.00251 ( 2) SS BOND : angle 1.26972 ( 4) covalent geometry : bond 0.00352 ( 3159) covalent geometry : angle 0.57137 ( 4305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.317 Fit side-chains REVERT: A 106 ASP cc_start: 0.8943 (t0) cc_final: 0.8497 (t0) REVERT: A 297 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7666 (t80) REVERT: D 50 VAL cc_start: 0.8513 (p) cc_final: 0.8309 (m) outliers start: 11 outliers final: 9 residues processed: 40 average time/residue: 0.0930 time to fit residues: 5.2720 Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.188176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128016 restraints weight = 3175.360| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.43 r_work: 0.3299 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3161 Z= 0.126 Angle : 0.529 6.256 4309 Z= 0.267 Chirality : 0.040 0.121 501 Planarity : 0.003 0.029 527 Dihedral : 3.576 21.547 456 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.11 % Allowed : 17.08 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.46), residues: 390 helix: 2.30 (0.38), residues: 200 sheet: 0.64 (0.82), residues: 52 loop : -2.76 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.017 0.001 PHE A 312 TYR 0.014 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.06718 ( 169) hydrogen bonds : angle 3.46561 ( 489) SS BOND : bond 0.00177 ( 2) SS BOND : angle 1.11724 ( 4) covalent geometry : bond 0.00263 ( 3159) covalent geometry : angle 0.52771 ( 4305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.328 Fit side-chains REVERT: A 106 ASP cc_start: 0.8790 (t0) cc_final: 0.8353 (t0) REVERT: A 297 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7663 (t80) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.0938 time to fit residues: 5.1596 Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.0000 chunk 24 optimal weight: 0.0070 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.189210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133871 restraints weight = 3206.049| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.19 r_work: 0.3326 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3161 Z= 0.118 Angle : 0.519 6.048 4309 Z= 0.262 Chirality : 0.040 0.120 501 Planarity : 0.003 0.029 527 Dihedral : 3.517 21.325 456 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.11 % Allowed : 17.39 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.46), residues: 390 helix: 2.47 (0.38), residues: 200 sheet: 0.84 (0.83), residues: 50 loop : -2.72 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.018 0.001 PHE A 312 TYR 0.013 0.001 TYR A 204 ARG 0.002 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.06291 ( 169) hydrogen bonds : angle 3.41140 ( 489) SS BOND : bond 0.00198 ( 2) SS BOND : angle 1.06901 ( 4) covalent geometry : bond 0.00237 ( 3159) covalent geometry : angle 0.51797 ( 4305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.337 Fit side-chains REVERT: A 106 ASP cc_start: 0.8711 (t0) cc_final: 0.8316 (t0) outliers start: 10 outliers final: 9 residues processed: 37 average time/residue: 0.1015 time to fit residues: 5.2234 Evaluate side-chains 43 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.187363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127155 restraints weight = 3163.398| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.42 r_work: 0.3288 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3161 Z= 0.129 Angle : 0.528 6.152 4309 Z= 0.268 Chirality : 0.040 0.121 501 Planarity : 0.003 0.028 527 Dihedral : 3.539 21.538 456 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.42 % Allowed : 16.77 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.46), residues: 390 helix: 2.46 (0.38), residues: 200 sheet: 0.73 (0.81), residues: 52 loop : -2.63 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.017 0.001 PHE A 312 TYR 0.014 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.06945 ( 169) hydrogen bonds : angle 3.46068 ( 489) SS BOND : bond 0.00203 ( 2) SS BOND : angle 1.06693 ( 4) covalent geometry : bond 0.00271 ( 3159) covalent geometry : angle 0.52745 ( 4305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.339 Fit side-chains REVERT: A 106 ASP cc_start: 0.8785 (t0) cc_final: 0.8344 (t0) REVERT: A 297 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7585 (t80) outliers start: 11 outliers final: 9 residues processed: 37 average time/residue: 0.1003 time to fit residues: 5.3441 Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.186991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126483 restraints weight = 3234.400| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.44 r_work: 0.3278 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3161 Z= 0.132 Angle : 0.532 6.215 4309 Z= 0.270 Chirality : 0.040 0.122 501 Planarity : 0.003 0.028 527 Dihedral : 3.552 21.676 456 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.42 % Allowed : 16.77 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.46), residues: 390 helix: 2.48 (0.38), residues: 200 sheet: 0.75 (0.82), residues: 52 loop : -2.62 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.017 0.001 PHE A 312 TYR 0.014 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.07092 ( 169) hydrogen bonds : angle 3.48005 ( 489) SS BOND : bond 0.00205 ( 2) SS BOND : angle 1.08515 ( 4) covalent geometry : bond 0.00279 ( 3159) covalent geometry : angle 0.53170 ( 4305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2132.57 seconds wall clock time: 37 minutes 14.55 seconds (2234.55 seconds total)