Starting phenix.real_space_refine on Sat May 10 07:58:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eah_47831/05_2025/9eah_47831.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eah_47831/05_2025/9eah_47831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eah_47831/05_2025/9eah_47831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eah_47831/05_2025/9eah_47831.map" model { file = "/net/cci-nas-00/data/ceres_data/9eah_47831/05_2025/9eah_47831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eah_47831/05_2025/9eah_47831.cif" } resolution = 3.1 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= 0.000 sd= 0.011 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 26 5.16 5 C 3673 2.51 5 N 902 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5606 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3024 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 935 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CLR': 1, 'OLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.51, per 1000 atoms: 0.80 Number of scatterers: 5606 At special positions: 0 Unit cell: (68.89, 96.28, 138.61, 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 26 16.00 O 1005 8.00 N 902 7.00 C 3673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 764.3 milliseconds 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 50.4% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 29 through 56 removed outlier: 4.083A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 90 removed outlier: 4.024A pdb=" N THR A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 96 through 132 removed outlier: 4.168A pdb=" N LEU A 100 " --> pdb=" O PHE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 204 through 245 removed outlier: 3.601A pdb=" N VAL A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.639A pdb=" N LYS A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 305 removed outlier: 3.644A pdb=" N PHE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.761A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 removed outlier: 3.934A pdb=" N ARG A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1269 Proline residue: A1255 - end of helix Processing helix chain 'A' and resid 1273 through 1292 removed outlier: 3.515A pdb=" N ILE A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Proline residue: A1285 - end of helix removed outlier: 3.798A pdb=" N TYR A1292 " --> pdb=" O ILE A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1305 removed outlier: 3.655A pdb=" N LEU A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Proline residue: A1299 - end of helix removed outlier: 3.824A pdb=" N TYR A1302 " --> pdb=" O ASN A1298 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A1303 " --> pdb=" O PRO A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1315 removed outlier: 3.532A pdb=" N PHE A1313 " --> pdb=" O PHE A1309 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 107 through 112 removed outlier: 4.229A pdb=" N TRP C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 4.085A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.601A pdb=" N LYS B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 8.377A pdb=" N VAL B 106 " --> pdb=" O CYS A 180 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE A 182 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 171 removed outlier: 8.377A pdb=" N VAL B 106 " --> pdb=" O CYS A 180 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE A 182 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.919A pdb=" N ALA C 82 " --> pdb=" O CYS C 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 62 through 63 removed outlier: 6.558A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR C 53 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N SER C 55 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE C 35 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.668A pdb=" N VAL D 20 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.870A pdb=" N LEU D 12 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.870A pdb=" N LEU D 12 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR D 99 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 23 343 hydrogen bonds defined for protein. 960 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: 1.82 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1704 1.34 - 1.46: 1501 1.46 - 1.58: 2508 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 5751 Sorted by residual: bond pdb=" C3 CLR A1402 " pdb=" O1 CLR A1402 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C SER C 57 " pdb=" N SER C 58 " ideal model delta sigma weight residual 1.332 1.321 0.012 1.40e-02 5.10e+03 6.91e-01 bond pdb=" CB VAL A 116 " pdb=" CG1 VAL A 116 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.44e-01 bond pdb=" CG PRO A 207 " pdb=" CD PRO A 207 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.35e-01 bond pdb=" C VAL A 108 " pdb=" O VAL A 108 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.12e-02 7.97e+03 4.41e-01 ... (remaining 5746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 7588 1.02 - 2.04: 189 2.04 - 3.05: 24 3.05 - 4.07: 13 4.07 - 5.09: 12 Bond angle restraints: 7826 Sorted by residual: angle pdb=" C SER D 51 " pdb=" N ALA D 52 " pdb=" CA ALA D 52 " ideal model delta sigma weight residual 121.54 125.72 -4.18 1.91e+00 2.74e-01 4.79e+00 angle pdb=" N GLU C 108 " pdb=" CA GLU C 108 " pdb=" C GLU C 108 " ideal model delta sigma weight residual 109.81 114.50 -4.69 2.21e+00 2.05e-01 4.51e+00 angle pdb=" N VAL A 131 " pdb=" CA VAL A 131 " pdb=" C VAL A 131 " ideal model delta sigma weight residual 109.34 112.78 -3.44 2.08e+00 2.31e-01 2.73e+00 angle pdb=" C SER D 31 " pdb=" N SER D 32 " pdb=" CA SER D 32 " ideal model delta sigma weight residual 121.54 118.54 3.00 1.91e+00 2.74e-01 2.47e+00 angle pdb=" C GLY C 107 " pdb=" N GLU C 108 " pdb=" CA GLU C 108 " ideal model delta sigma weight residual 121.80 125.51 -3.71 2.44e+00 1.68e-01 2.32e+00 ... (remaining 7821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 3174 16.20 - 32.39: 168 32.39 - 48.59: 38 48.59 - 64.78: 3 64.78 - 80.98: 6 Dihedral angle restraints: 3389 sinusoidal: 1336 harmonic: 2053 Sorted by residual: dihedral pdb=" CA TYR C 104 " pdb=" C TYR C 104 " pdb=" N TRP C 105 " pdb=" CA TRP C 105 " ideal model delta harmonic sigma weight residual 180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASN B 76 " pdb=" CB ASN B 76 " pdb=" CG ASN B 76 " pdb=" OD1 ASN B 76 " ideal model delta sinusoidal sigma weight residual -90.00 -157.49 67.49 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA TYR A 326 " pdb=" C TYR A 326 " pdb=" N ILE A 327 " pdb=" CA ILE A 327 " ideal model delta harmonic sigma weight residual -180.00 -165.09 -14.91 0 5.00e+00 4.00e-02 8.89e+00 ... (remaining 3386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 494 0.026 - 0.052: 248 0.052 - 0.079: 83 0.079 - 0.105: 43 0.105 - 0.131: 13 Chirality restraints: 881 Sorted by residual: chirality pdb=" CA TRP C 105 " pdb=" N TRP C 105 " pdb=" C TRP C 105 " pdb=" CB TRP C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE D 22 " pdb=" N ILE D 22 " pdb=" C ILE D 22 " pdb=" CB ILE D 22 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 878 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 108 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO C 109 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 29 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C PHE B 29 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE B 29 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR B 30 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 95 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.018 5.00e-02 4.00e+02 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1276 2.78 - 3.31: 5250 3.31 - 3.84: 9265 3.84 - 4.37: 11426 4.37 - 4.90: 20022 Nonbonded interactions: 47239 Sorted by model distance: nonbonded pdb=" NE2 GLN D 91 " pdb=" O LEU D 97 " model vdw 2.254 3.120 nonbonded pdb=" O GLY C 103 " pdb=" OH TYR D 95 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 52 " pdb=" OG1 THR B 56 " model vdw 2.262 3.040 nonbonded pdb=" O THR A 234 " pdb=" ND2 ASN A 238 " model vdw 2.274 3.120 nonbonded pdb=" OG SER B 17 " pdb=" O MET B 82 " model vdw 2.281 3.040 ... (remaining 47234 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: 2.520 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.002 0.031 5755 Z= 0.112 Angle : 0.447 5.089 7834 Z= 0.232 Chirality : 0.039 0.131 881 Planarity : 0.003 0.044 959 Dihedral : 10.948 80.980 2061 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.68 % Allowed : 5.42 % Favored : 93.90 % 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: -0.11 (0.34), residues: 688 helix: 0.07 (0.30), residues: 309 sheet: 0.56 (0.47), residues: 141 loop : -0.43 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 232 HIS 0.001 0.000 HIS A1256 PHE 0.012 0.001 PHE A 44 TYR 0.012 0.001 TYR D 92 ARG 0.001 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.21892 ( 333) hydrogen bonds : angle 8.00176 ( 960) SS BOND : bond 0.00166 ( 4) SS BOND : angle 1.20457 ( 8) covalent geometry : bond 0.00249 ( 5751) covalent geometry : angle 0.44590 ( 7826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.550 Fit side-chains REVERT: A 57 MET cc_start: 0.7808 (mmt) cc_final: 0.7037 (mtp) REVERT: A 237 ASP cc_start: 0.7078 (m-30) cc_final: 0.6789 (m-30) REVERT: A 1288 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7993 (tt) REVERT: C 39 TRP cc_start: 0.8293 (m100) cc_final: 0.7994 (m100) REVERT: C 68 LYS cc_start: 0.7521 (ttmm) cc_final: 0.7241 (ttpt) REVERT: B 72 ASP cc_start: 0.6796 (t0) cc_final: 0.5785 (m-30) REVERT: B 77 THR cc_start: 0.7140 (m) cc_final: 0.6882 (m) REVERT: B 95 CYS cc_start: 0.8463 (p) cc_final: 0.8084 (p) outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 0.1602 time to fit residues: 16.7201 Evaluate side-chains 70 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain B residue 92 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN D 4 GLN B 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.196620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149910 restraints weight = 5778.263| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.60 r_work: 0.3295 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5755 Z= 0.150 Angle : 0.513 5.070 7834 Z= 0.276 Chirality : 0.041 0.131 881 Planarity : 0.004 0.052 959 Dihedral : 6.433 71.167 846 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.20 % Allowed : 6.44 % Favored : 91.36 % 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: 0.54 (0.33), residues: 688 helix: 1.07 (0.29), residues: 314 sheet: 0.15 (0.44), residues: 152 loop : -0.35 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.020 0.001 PHE A 44 TYR 0.012 0.001 TYR A 87 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 333) hydrogen bonds : angle 5.15736 ( 960) SS BOND : bond 0.00262 ( 4) SS BOND : angle 1.42739 ( 8) covalent geometry : bond 0.00335 ( 5751) covalent geometry : angle 0.51148 ( 7826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.590 Fit side-chains REVERT: A 237 ASP cc_start: 0.6949 (m-30) cc_final: 0.6608 (m-30) REVERT: A 253 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: A 1288 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7737 (tt) REVERT: C 39 TRP cc_start: 0.8338 (m100) cc_final: 0.8134 (m100) REVERT: C 70 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7715 (mtm-85) REVERT: B 22 CYS cc_start: 0.7277 (t) cc_final: 0.6657 (t) REVERT: B 56 THR cc_start: 0.8093 (p) cc_final: 0.7864 (t) REVERT: B 72 ASP cc_start: 0.6774 (t0) cc_final: 0.5740 (m-30) REVERT: B 77 THR cc_start: 0.7098 (m) cc_final: 0.6783 (m) outliers start: 13 outliers final: 5 residues processed: 85 average time/residue: 0.1679 time to fit residues: 19.0073 Evaluate side-chains 76 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1297 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain B residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 43 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 50 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1294 ASN B 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.199443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151924 restraints weight = 5782.356| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.28 r_work: 0.3323 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5755 Z= 0.112 Angle : 0.459 5.098 7834 Z= 0.244 Chirality : 0.039 0.124 881 Planarity : 0.004 0.070 959 Dihedral : 6.318 71.368 846 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.37 % Allowed : 8.14 % Favored : 89.49 % 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: 0.87 (0.33), residues: 688 helix: 1.57 (0.29), residues: 313 sheet: 0.17 (0.44), residues: 152 loop : -0.44 (0.46), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.017 0.001 PHE A 44 TYR 0.009 0.001 TYR D 92 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 333) hydrogen bonds : angle 4.71162 ( 960) SS BOND : bond 0.00208 ( 4) SS BOND : angle 1.09292 ( 8) covalent geometry : bond 0.00237 ( 5751) covalent geometry : angle 0.45807 ( 7826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.626 Fit side-chains REVERT: A 237 ASP cc_start: 0.6945 (m-30) cc_final: 0.6604 (m-30) REVERT: A 306 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8017 (mt-10) REVERT: A 1288 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7874 (tt) REVERT: C 70 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7775 (mtm-85) REVERT: B 56 THR cc_start: 0.8100 (p) cc_final: 0.7884 (t) REVERT: B 72 ASP cc_start: 0.6805 (t0) cc_final: 0.5754 (m-30) REVERT: B 77 THR cc_start: 0.7118 (m) cc_final: 0.6879 (m) outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 0.1825 time to fit residues: 19.9898 Evaluate side-chains 77 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 12 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.198502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152820 restraints weight = 5912.618| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.34 r_work: 0.3297 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5755 Z= 0.131 Angle : 0.469 5.031 7834 Z= 0.249 Chirality : 0.040 0.126 881 Planarity : 0.004 0.053 959 Dihedral : 6.269 70.989 846 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.71 % Allowed : 8.14 % Favored : 89.15 % 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: 0.92 (0.33), residues: 688 helix: 1.64 (0.29), residues: 314 sheet: 0.14 (0.43), residues: 153 loop : -0.44 (0.46), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.015 0.001 PHE A 44 TYR 0.012 0.001 TYR B 93 ARG 0.009 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 333) hydrogen bonds : angle 4.59687 ( 960) SS BOND : bond 0.00220 ( 4) SS BOND : angle 1.08846 ( 8) covalent geometry : bond 0.00297 ( 5751) covalent geometry : angle 0.46836 ( 7826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.575 Fit side-chains REVERT: A 237 ASP cc_start: 0.6902 (m-30) cc_final: 0.6566 (m-30) REVERT: A 253 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: A 1288 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7812 (tt) REVERT: C 70 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7771 (mtm-85) REVERT: B 56 THR cc_start: 0.8156 (p) cc_final: 0.7932 (t) REVERT: B 72 ASP cc_start: 0.6801 (t0) cc_final: 0.5780 (m-30) REVERT: B 77 THR cc_start: 0.7315 (m) cc_final: 0.7042 (m) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.1578 time to fit residues: 18.9181 Evaluate side-chains 84 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 13 optimal weight: 0.0370 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.199254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151506 restraints weight = 5770.203| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.26 r_work: 0.3298 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5755 Z= 0.135 Angle : 0.472 5.087 7834 Z= 0.250 Chirality : 0.040 0.126 881 Planarity : 0.004 0.053 959 Dihedral : 6.274 70.800 846 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.37 % Allowed : 9.32 % Favored : 88.31 % 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: 0.95 (0.33), residues: 688 helix: 1.74 (0.29), residues: 314 sheet: 0.08 (0.43), residues: 153 loop : -0.49 (0.45), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.015 0.001 PHE A 44 TYR 0.013 0.001 TYR B 93 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 333) hydrogen bonds : angle 4.52603 ( 960) SS BOND : bond 0.00218 ( 4) SS BOND : angle 1.09447 ( 8) covalent geometry : bond 0.00306 ( 5751) covalent geometry : angle 0.47120 ( 7826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.571 Fit side-chains REVERT: A 173 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 237 ASP cc_start: 0.6891 (m-30) cc_final: 0.6511 (m-30) REVERT: A 253 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: A 1288 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7795 (tt) REVERT: C 70 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7841 (mtm-85) REVERT: B 56 THR cc_start: 0.8149 (p) cc_final: 0.7916 (t) REVERT: B 72 ASP cc_start: 0.6835 (t0) cc_final: 0.5787 (m-30) REVERT: B 77 THR cc_start: 0.7368 (m) cc_final: 0.7094 (m) outliers start: 14 outliers final: 10 residues processed: 92 average time/residue: 0.1605 time to fit residues: 19.7123 Evaluate side-chains 87 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.198404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150392 restraints weight = 5781.496| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.28 r_work: 0.3270 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5755 Z= 0.137 Angle : 0.471 5.051 7834 Z= 0.250 Chirality : 0.040 0.127 881 Planarity : 0.004 0.055 959 Dihedral : 6.270 70.592 846 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.37 % Allowed : 10.34 % Favored : 87.29 % 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: 0.94 (0.33), residues: 688 helix: 1.75 (0.29), residues: 314 sheet: 0.09 (0.43), residues: 153 loop : -0.53 (0.45), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.014 0.001 PHE A 44 TYR 0.011 0.001 TYR A 87 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 333) hydrogen bonds : angle 4.50662 ( 960) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.09782 ( 8) covalent geometry : bond 0.00315 ( 5751) covalent geometry : angle 0.46974 ( 7826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.555 Fit side-chains REVERT: A 198 THR cc_start: 0.8494 (m) cc_final: 0.8146 (m) REVERT: A 237 ASP cc_start: 0.6901 (m-30) cc_final: 0.6559 (m-30) REVERT: A 253 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: A 1288 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7854 (tt) REVERT: C 70 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7864 (mtm-85) REVERT: B 38 ARG cc_start: 0.8411 (ptp90) cc_final: 0.8111 (ptp-170) REVERT: B 56 THR cc_start: 0.8167 (p) cc_final: 0.7926 (t) REVERT: B 72 ASP cc_start: 0.6813 (t0) cc_final: 0.5795 (m-30) REVERT: B 77 THR cc_start: 0.7413 (m) cc_final: 0.7140 (m) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.1607 time to fit residues: 19.0868 Evaluate side-chains 90 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.198320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.150035 restraints weight = 5798.286| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.29 r_work: 0.3306 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5755 Z= 0.136 Angle : 0.470 5.092 7834 Z= 0.249 Chirality : 0.040 0.126 881 Planarity : 0.004 0.055 959 Dihedral : 6.277 70.450 846 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.54 % Allowed : 10.51 % Favored : 86.95 % 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: 0.95 (0.33), residues: 688 helix: 1.76 (0.29), residues: 314 sheet: 0.09 (0.43), residues: 153 loop : -0.55 (0.45), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.014 0.001 PHE A 44 TYR 0.011 0.001 TYR A 87 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 333) hydrogen bonds : angle 4.47010 ( 960) SS BOND : bond 0.00220 ( 4) SS BOND : angle 1.13403 ( 8) covalent geometry : bond 0.00313 ( 5751) covalent geometry : angle 0.46891 ( 7826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.591 Fit side-chains REVERT: A 198 THR cc_start: 0.8483 (m) cc_final: 0.8143 (m) REVERT: A 237 ASP cc_start: 0.6796 (m-30) cc_final: 0.6440 (m-30) REVERT: A 253 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: A 310 LYS cc_start: 0.7823 (mmmm) cc_final: 0.7573 (mmtm) REVERT: A 1288 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7844 (tt) REVERT: C 70 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7883 (mtm-85) REVERT: B 38 ARG cc_start: 0.8370 (ptp90) cc_final: 0.8067 (ptp-170) REVERT: B 56 THR cc_start: 0.8171 (p) cc_final: 0.7929 (t) REVERT: B 72 ASP cc_start: 0.6819 (t0) cc_final: 0.5807 (m-30) REVERT: B 77 THR cc_start: 0.7408 (m) cc_final: 0.7148 (m) outliers start: 15 outliers final: 8 residues processed: 93 average time/residue: 0.1706 time to fit residues: 21.0225 Evaluate side-chains 88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain B residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 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 = 0.4194 r_free = 0.4194 target = 0.197081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148334 restraints weight = 5758.904| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.27 r_work: 0.3285 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5755 Z= 0.169 Angle : 0.499 5.181 7834 Z= 0.265 Chirality : 0.041 0.132 881 Planarity : 0.004 0.056 959 Dihedral : 6.360 70.300 846 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.03 % Allowed : 11.53 % Favored : 86.44 % 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 (0.33), residues: 688 helix: 1.66 (0.28), residues: 314 sheet: 0.04 (0.43), residues: 153 loop : -0.56 (0.45), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.003 0.001 HIS A1256 PHE 0.013 0.001 PHE A 44 TYR 0.013 0.002 TYR A 87 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 333) hydrogen bonds : angle 4.53869 ( 960) SS BOND : bond 0.00257 ( 4) SS BOND : angle 1.23348 ( 8) covalent geometry : bond 0.00399 ( 5751) covalent geometry : angle 0.49798 ( 7826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.609 Fit side-chains REVERT: A 198 THR cc_start: 0.8479 (m) cc_final: 0.8124 (m) REVERT: A 237 ASP cc_start: 0.6830 (m-30) cc_final: 0.6485 (m-30) REVERT: A 253 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: A 310 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7570 (mmtm) REVERT: A 1288 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7831 (tt) REVERT: C 70 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.7889 (mtm-85) REVERT: B 38 ARG cc_start: 0.8373 (ptp90) cc_final: 0.8063 (ptp-170) REVERT: B 56 THR cc_start: 0.8181 (p) cc_final: 0.7940 (t) REVERT: B 72 ASP cc_start: 0.6794 (t0) cc_final: 0.5877 (m-30) REVERT: B 77 THR cc_start: 0.7615 (m) cc_final: 0.7346 (m) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.1862 time to fit residues: 21.8350 Evaluate side-chains 88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.195691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148863 restraints weight = 5806.592| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.32 r_work: 0.3289 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5755 Z= 0.149 Angle : 0.485 5.168 7834 Z= 0.257 Chirality : 0.041 0.131 881 Planarity : 0.004 0.055 959 Dihedral : 6.387 70.386 846 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.20 % Allowed : 11.53 % Favored : 86.27 % 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: 0.90 (0.33), residues: 688 helix: 1.72 (0.28), residues: 314 sheet: 0.10 (0.43), residues: 152 loop : -0.59 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.013 0.001 PHE A 44 TYR 0.012 0.001 TYR B 32 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 333) hydrogen bonds : angle 4.49456 ( 960) SS BOND : bond 0.00241 ( 4) SS BOND : angle 1.16121 ( 8) covalent geometry : bond 0.00347 ( 5751) covalent geometry : angle 0.48404 ( 7826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.601 Fit side-chains REVERT: A 198 THR cc_start: 0.8636 (m) cc_final: 0.8284 (m) REVERT: A 253 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: A 310 LYS cc_start: 0.7878 (mmmm) cc_final: 0.7634 (mmtm) REVERT: A 1288 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8010 (tt) REVERT: C 70 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8148 (mtm-85) REVERT: B 38 ARG cc_start: 0.8481 (ptp90) cc_final: 0.8212 (ptp-170) REVERT: B 56 THR cc_start: 0.8246 (p) cc_final: 0.8008 (t) REVERT: B 72 ASP cc_start: 0.6764 (t0) cc_final: 0.5927 (m-30) REVERT: B 77 THR cc_start: 0.7678 (m) cc_final: 0.7473 (m) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.1749 time to fit residues: 20.3141 Evaluate side-chains 85 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN D 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.196209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149608 restraints weight = 5844.305| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.33 r_work: 0.3303 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5755 Z= 0.135 Angle : 0.475 5.091 7834 Z= 0.252 Chirality : 0.040 0.131 881 Planarity : 0.004 0.055 959 Dihedral : 6.355 70.392 846 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.86 % Allowed : 11.86 % Favored : 86.27 % 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: 0.91 (0.33), residues: 688 helix: 1.74 (0.28), residues: 314 sheet: 0.11 (0.43), residues: 151 loop : -0.61 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.013 0.001 PHE A 44 TYR 0.015 0.001 TYR B 32 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 333) hydrogen bonds : angle 4.45199 ( 960) SS BOND : bond 0.00214 ( 4) SS BOND : angle 1.13955 ( 8) covalent geometry : bond 0.00310 ( 5751) covalent geometry : angle 0.47394 ( 7826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.544 Fit side-chains REVERT: A 198 THR cc_start: 0.8645 (m) cc_final: 0.8282 (m) REVERT: A 237 ASP cc_start: 0.6924 (m-30) cc_final: 0.6667 (m-30) REVERT: A 253 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: A 310 LYS cc_start: 0.7865 (mmmm) cc_final: 0.7623 (mmtm) REVERT: A 1288 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8003 (tt) REVERT: C 70 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.8178 (mtm-85) REVERT: B 38 ARG cc_start: 0.8474 (ptp90) cc_final: 0.8231 (ptp-170) REVERT: B 56 THR cc_start: 0.8248 (p) cc_final: 0.8005 (t) REVERT: B 72 ASP cc_start: 0.6764 (t0) cc_final: 0.5921 (m-30) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.1895 time to fit residues: 21.4096 Evaluate side-chains 85 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.197304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150401 restraints weight = 5843.510| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.57 r_work: 0.3291 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5755 Z= 0.157 Angle : 0.493 5.162 7834 Z= 0.262 Chirality : 0.041 0.132 881 Planarity : 0.004 0.055 959 Dihedral : 6.393 70.234 846 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.69 % Allowed : 12.03 % Favored : 86.27 % 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: 0.84 (0.33), residues: 688 helix: 1.68 (0.28), residues: 314 sheet: 0.06 (0.43), residues: 151 loop : -0.62 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.013 0.001 PHE A 44 TYR 0.012 0.002 TYR A 87 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 333) hydrogen bonds : angle 4.49666 ( 960) SS BOND : bond 0.00233 ( 4) SS BOND : angle 1.48525 ( 8) covalent geometry : bond 0.00367 ( 5751) covalent geometry : angle 0.49091 ( 7826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3291.73 seconds wall clock time: 58 minutes 1.87 seconds (3481.87 seconds total)