Starting phenix.real_space_refine on Fri Jul 3 10:58:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opp_17084/07_2026/8opp_17084_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opp_17084/07_2026/8opp_17084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8opp_17084/07_2026/8opp_17084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opp_17084/07_2026/8opp_17084.map" model { file = "/net/cci-nas-00/data/ceres_data/8opp_17084/07_2026/8opp_17084_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opp_17084/07_2026/8opp_17084_trim.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2545 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 27 5.49 5 S 27 5.16 5 C 3737 2.51 5 N 1001 2.21 5 O 1150 1.98 5 H 5730 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11672 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 10844 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 36, 'TRANS': 633} Chain breaks: 7 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 799 Classifications: {'RNA': 25} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 23} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'P5E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.02, per 1000 atoms: 0.17 Number of scatterers: 11672 At special positions: 0 Unit cell: (84.812, 88.54, 113.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 27 15.00 O 1150 8.00 N 1001 7.00 C 3737 6.00 H 5730 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.20 Conformation dependent library (CDL) restraints added in 460.4 milliseconds 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 47.8% alpha, 8.4% beta 4 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 288 through 305 removed outlier: 3.507A pdb=" N ALA A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 327 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 458 through 473 Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 550 through 564 removed outlier: 3.551A pdb=" N LEU A 554 " --> pdb=" O PRO A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.956A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 630 Processing helix chain 'A' and resid 994 through 1013 Processing helix chain 'A' and resid 1015 through 1035 removed outlier: 3.831A pdb=" N GLN A1035 " --> pdb=" O SER A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1090 Processing helix chain 'A' and resid 1125 through 1141 removed outlier: 3.532A pdb=" N HIS A1129 " --> pdb=" O THR A1125 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A1134 " --> pdb=" O ASN A1130 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A1141 " --> pdb=" O TYR A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1159 removed outlier: 3.707A pdb=" N LYS A1145 " --> pdb=" O ASP A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1184 Processing helix chain 'A' and resid 1219 through 1224 removed outlier: 3.703A pdb=" N TYR A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1247 Processing helix chain 'A' and resid 1265 through 1269 Processing helix chain 'A' and resid 1293 through 1313 removed outlier: 3.561A pdb=" N ILE A1313 " --> pdb=" O ARG A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1329 removed outlier: 3.561A pdb=" N PHE A1329 " --> pdb=" O LYS A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1336 Processing sheet with id=AA1, first strand: chain 'A' and resid 335 through 338 removed outlier: 3.906A pdb=" N SER A 335 " --> pdb=" O GLN A 358 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 353 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER A 410 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 355 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL A 395 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A 387 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 397 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL A 385 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 399 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 498 through 503 removed outlier: 5.168A pdb=" N LEU A 499 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A 510 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A 501 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 537 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1041 through 1045 removed outlier: 4.428A pdb=" N ASP A1060 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A1059 " --> pdb=" O ASP A1119 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER A1121 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A1061 " --> pdb=" O SER A1121 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A1108 " --> pdb=" O LEU A1097 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.10: 5713 1.10 - 1.35: 1840 1.35 - 1.61: 4260 1.61 - 1.87: 41 1.87 - 2.13: 1 Bond restraints: 11855 Sorted by residual: bond pdb=" C2' P5E A1501 " pdb=" C3' P5E A1501 " ideal model delta sigma weight residual 1.529 1.270 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C5 P5E A1501 " pdb=" C6 P5E A1501 " ideal model delta sigma weight residual 1.342 1.491 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" C1' P5E A1501 " pdb=" C2' P5E A1501 " ideal model delta sigma weight residual 1.526 1.670 -0.144 2.00e-02 2.50e+03 5.22e+01 bond pdb=" O3B P5E A1501 " pdb=" PG P5E A1501 " ideal model delta sigma weight residual 1.789 1.649 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C4' P5E A1501 " pdb=" C5' P5E A1501 " ideal model delta sigma weight residual 1.517 1.380 0.137 2.00e-02 2.50e+03 4.71e+01 ... (remaining 11850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 21348 2.55 - 5.09: 99 5.09 - 7.64: 18 7.64 - 10.18: 4 10.18 - 12.73: 3 Bond angle restraints: 21472 Sorted by residual: angle pdb=" O3A P5E A1501 " pdb=" PA P5E A1501 " pdb=" S1A P5E A1501 " ideal model delta sigma weight residual 97.53 110.26 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O2A P5E A1501 " pdb=" PA P5E A1501 " pdb=" O3A P5E A1501 " ideal model delta sigma weight residual 122.05 109.71 12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O1B P5E A1501 " pdb=" PB P5E A1501 " pdb=" O2B P5E A1501 " ideal model delta sigma weight residual 119.71 109.37 10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CA PRO A1187 " pdb=" N PRO A1187 " pdb=" CD PRO A1187 " ideal model delta sigma weight residual 112.00 107.30 4.70 1.40e+00 5.10e-01 1.13e+01 angle pdb=" O2G P5E A1501 " pdb=" PG P5E A1501 " pdb=" O3B P5E A1501 " ideal model delta sigma weight residual 99.38 109.42 -10.04 3.00e+00 1.11e-01 1.12e+01 ... (remaining 21467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 4883 18.11 - 36.22: 483 36.22 - 54.33: 164 54.33 - 72.45: 52 72.45 - 90.56: 13 Dihedral angle restraints: 5595 sinusoidal: 3256 harmonic: 2339 Sorted by residual: dihedral pdb=" O4' C D 68 " pdb=" C1' C D 68 " pdb=" N1 C D 68 " pdb=" C2 C D 68 " ideal model delta sinusoidal sigma weight residual 232.00 179.52 52.48 1 1.70e+01 3.46e-03 1.30e+01 dihedral pdb=" CA ASN A1185 " pdb=" C ASN A1185 " pdb=" N PRO A1186 " pdb=" CA PRO A1186 " ideal model delta harmonic sigma weight residual 180.00 163.35 16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" N GLN A1216 " pdb=" CA GLN A1216 " pdb=" CB GLN A1216 " pdb=" CG GLN A1216 " ideal model delta sinusoidal sigma weight residual -180.00 -120.55 -59.45 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 970 0.134 - 0.268: 2 0.268 - 0.401: 1 0.401 - 0.535: 0 0.535 - 0.669: 1 Chirality restraints: 974 Sorted by residual: chirality pdb=" PA P5E A1501 " pdb=" O2A P5E A1501 " pdb=" O3A P5E A1501 " pdb=" O5' P5E A1501 " both_signs ideal model delta sigma weight residual True 2.40 -3.07 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C3' P5E A1501 " pdb=" C2' P5E A1501 " pdb=" C4' P5E A1501 " pdb=" O3' P5E A1501 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C4' P5E A1501 " pdb=" C3' P5E A1501 " pdb=" C5' P5E A1501 " pdb=" O4' P5E A1501 " both_signs ideal model delta sigma weight residual False -2.42 -2.66 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 971 not shown) Planarity restraints: 1609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1186 " 0.053 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO A1187 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A1187 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1187 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1165 " -0.112 9.50e-02 1.11e+02 3.77e-02 1.94e+00 pdb=" NE ARG A1165 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A1165 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A1165 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A1165 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A1165 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A1165 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A1165 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A1165 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 612 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 613 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 613 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 613 " 0.018 5.00e-02 4.00e+02 ... (remaining 1606 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.28: 2036 2.28 - 2.86: 26294 2.86 - 3.44: 30573 3.44 - 4.02: 41291 4.02 - 4.60: 61156 Nonbonded interactions: 161350 Sorted by model distance: nonbonded pdb=" O GLY A 340 " pdb=" HG SER A 344 " model vdw 1.694 2.450 nonbonded pdb=" O PRO A1332 " pdb=" HG1 THR A1336 " model vdw 1.718 2.450 nonbonded pdb=" OP1 C D 67 " pdb="HO2' C D 68 " model vdw 1.740 2.450 nonbonded pdb=" O ILE A1160 " pdb=" HH TYR A1173 " model vdw 1.785 2.450 nonbonded pdb=" O ASP A 380 " pdb=" HZ3 LYS A 401 " model vdw 1.788 2.450 ... (remaining 161345 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 group one per residue 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.070 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.490 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 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 : 0.007 0.259 6125 Z= 0.339 Angle : 0.627 12.727 8410 Z= 0.286 Chirality : 0.045 0.669 974 Planarity : 0.004 0.078 963 Dihedral : 18.086 90.557 2447 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 18.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.34), residues: 654 helix: 2.69 (0.31), residues: 287 sheet: 0.53 (0.62), residues: 74 loop : -0.07 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1165 TYR 0.005 0.001 TYR A1245 PHE 0.007 0.001 PHE A 469 TRP 0.006 0.001 TRP A 509 HIS 0.001 0.000 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.34 ( 6125) covalent geometry : angle 0.62683 / 0.29 ( 8410) hydrogen bonds : bond 0.10631 / 7.82 ( 254) hydrogen bonds : angle 4.71625 / 3.50 ( 721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1132 ARG cc_start: 0.5992 (ttp80) cc_final: 0.5783 (ttp80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1948 time to fit residues: 19.8058 Evaluate side-chains 75 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.190713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.172856 restraints weight = 31076.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.177908 restraints weight = 14629.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.181051 restraints weight = 8203.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.183032 restraints weight = 5249.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.184429 restraints weight = 3705.157| |-----------------------------------------------------------------------------| r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6125 Z= 0.158 Angle : 0.503 4.751 8410 Z= 0.260 Chirality : 0.039 0.259 974 Planarity : 0.004 0.053 963 Dihedral : 15.283 93.380 1112 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.33 % Allowed : 18.60 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.33), residues: 654 helix: 2.30 (0.30), residues: 291 sheet: 0.58 (0.63), residues: 76 loop : -0.31 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1165 TYR 0.009 0.001 TYR A1245 PHE 0.014 0.001 PHE A1110 TRP 0.005 0.001 TRP A 555 HIS 0.008 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6125) covalent geometry : angle 0.50255 / 0.26 ( 8410) hydrogen bonds : bond 0.04217 / 2.93 ( 254) hydrogen bonds : angle 4.30542 / 3.19 ( 721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.5016 (mt) outliers start: 8 outliers final: 7 residues processed: 81 average time/residue: 0.1895 time to fit residues: 19.6185 Evaluate side-chains 84 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.183423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.164997 restraints weight = 30950.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.169984 restraints weight = 14758.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.173115 restraints weight = 8425.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.174932 restraints weight = 5449.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.176399 restraints weight = 3985.879| |-----------------------------------------------------------------------------| r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6125 Z= 0.246 Angle : 0.617 6.319 8410 Z= 0.330 Chirality : 0.041 0.150 974 Planarity : 0.005 0.050 963 Dihedral : 15.375 103.070 1112 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.66 % Allowed : 17.61 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.32), residues: 654 helix: 1.19 (0.28), residues: 291 sheet: -0.14 (0.63), residues: 76 loop : -0.83 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 399 TYR 0.016 0.003 TYR A1245 PHE 0.018 0.002 PHE A 389 TRP 0.010 0.002 TRP A1238 HIS 0.010 0.002 HIS A1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 ( 6125) covalent geometry : angle 0.61695 / 0.33 ( 8410) hydrogen bonds : bond 0.05502 / 3.74 ( 254) hydrogen bonds : angle 4.68349 / 3.46 ( 721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ASP cc_start: 0.8237 (p0) cc_final: 0.7979 (p0) REVERT: A 446 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.5132 (mt) REVERT: A 1165 ARG cc_start: 0.8124 (mmp80) cc_final: 0.7874 (mmp80) outliers start: 16 outliers final: 11 residues processed: 92 average time/residue: 0.1774 time to fit residues: 21.0316 Evaluate side-chains 96 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1180 PHE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.186433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.168293 restraints weight = 30900.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.173332 restraints weight = 14724.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.176444 restraints weight = 8350.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.178446 restraints weight = 5356.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.179469 restraints weight = 3812.542| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6125 Z= 0.119 Angle : 0.503 4.438 8410 Z= 0.263 Chirality : 0.038 0.146 974 Planarity : 0.004 0.039 963 Dihedral : 15.255 101.261 1112 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.33 % Allowed : 19.10 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.32), residues: 654 helix: 1.55 (0.29), residues: 291 sheet: 0.16 (0.63), residues: 76 loop : -0.68 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.010 0.001 TYR A1173 PHE 0.022 0.001 PHE A1110 TRP 0.014 0.002 TRP A1209 HIS 0.003 0.001 HIS A1090 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6125) covalent geometry : angle 0.50276 / 0.26 ( 8410) hydrogen bonds : bond 0.04030 / 2.70 ( 254) hydrogen bonds : angle 4.40334 / 3.25 ( 721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 ASP cc_start: 0.8193 (p0) cc_final: 0.7873 (p0) REVERT: A 446 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.5156 (mt) outliers start: 14 outliers final: 11 residues processed: 90 average time/residue: 0.1779 time to fit residues: 20.4565 Evaluate side-chains 93 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1185 ASN Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.185170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.167195 restraints weight = 30492.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.172097 restraints weight = 14618.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.175167 restraints weight = 8367.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.177164 restraints weight = 5417.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.178219 restraints weight = 3845.345| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6125 Z= 0.151 Angle : 0.507 4.467 8410 Z= 0.267 Chirality : 0.038 0.147 974 Planarity : 0.004 0.062 963 Dihedral : 15.210 101.806 1112 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.83 % Allowed : 19.93 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.32), residues: 654 helix: 1.55 (0.29), residues: 291 sheet: 0.14 (0.63), residues: 76 loop : -0.69 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.010 0.002 TYR A1137 PHE 0.010 0.001 PHE A1032 TRP 0.010 0.002 TRP A 443 HIS 0.004 0.001 HIS A1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 6125) covalent geometry : angle 0.50716 / 0.27 ( 8410) hydrogen bonds : bond 0.04004 / 2.70 ( 254) hydrogen bonds : angle 4.41871 / 3.26 ( 721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7537 (mmt180) REVERT: A 352 ASP cc_start: 0.8233 (p0) cc_final: 0.7876 (p0) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1872 time to fit residues: 21.9086 Evaluate side-chains 97 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.186010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.167833 restraints weight = 30960.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.172798 restraints weight = 14902.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.175918 restraints weight = 8543.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.177919 restraints weight = 5523.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.179297 restraints weight = 3925.758| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6125 Z= 0.123 Angle : 0.492 4.966 8410 Z= 0.259 Chirality : 0.038 0.147 974 Planarity : 0.004 0.037 963 Dihedral : 15.124 101.812 1112 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.99 % Allowed : 20.43 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.33), residues: 654 helix: 1.66 (0.29), residues: 291 sheet: 0.21 (0.63), residues: 76 loop : -0.63 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.008 0.001 TYR A1173 PHE 0.011 0.001 PHE A1244 TRP 0.009 0.001 TRP A 443 HIS 0.003 0.001 HIS A1090 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 6125) covalent geometry : angle 0.49180 / 0.26 ( 8410) hydrogen bonds : bond 0.03685 / 2.49 ( 254) hydrogen bonds : angle 4.31484 / 3.19 ( 721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7505 (mmt180) REVERT: A 352 ASP cc_start: 0.8206 (p0) cc_final: 0.7888 (p0) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.1859 time to fit residues: 21.5580 Evaluate side-chains 96 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1185 ASN Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.186047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.168385 restraints weight = 30678.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.173228 restraints weight = 14817.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.176274 restraints weight = 8480.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.178238 restraints weight = 5474.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.179462 restraints weight = 3882.778| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6125 Z= 0.123 Angle : 0.493 5.314 8410 Z= 0.258 Chirality : 0.038 0.147 974 Planarity : 0.004 0.034 963 Dihedral : 15.059 102.270 1112 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.66 % Allowed : 20.93 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.33), residues: 654 helix: 1.71 (0.29), residues: 291 sheet: 0.29 (0.65), residues: 76 loop : -0.63 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 399 TYR 0.009 0.001 TYR A1173 PHE 0.011 0.001 PHE A1032 TRP 0.009 0.001 TRP A 509 HIS 0.007 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6125) covalent geometry : angle 0.49259 / 0.26 ( 8410) hydrogen bonds : bond 0.03610 / 2.45 ( 254) hydrogen bonds : angle 4.28093 / 3.16 ( 721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7526 (mmt180) REVERT: A 352 ASP cc_start: 0.8231 (p0) cc_final: 0.7877 (p0) REVERT: A 604 ASN cc_start: 0.6388 (t0) cc_final: 0.6169 (t0) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.2015 time to fit residues: 22.5575 Evaluate side-chains 92 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1050 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.183603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.165267 restraints weight = 30427.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.170337 restraints weight = 14581.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.173484 restraints weight = 8293.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.175456 restraints weight = 5352.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.176802 restraints weight = 3831.511| |-----------------------------------------------------------------------------| r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6125 Z= 0.172 Angle : 0.532 5.212 8410 Z= 0.282 Chirality : 0.039 0.144 974 Planarity : 0.004 0.033 963 Dihedral : 15.095 105.223 1112 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.16 % Allowed : 20.93 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.33), residues: 654 helix: 1.45 (0.29), residues: 291 sheet: 0.15 (0.65), residues: 76 loop : -0.79 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 399 TYR 0.013 0.002 TYR A1245 PHE 0.014 0.002 PHE A1244 TRP 0.007 0.002 TRP A 443 HIS 0.009 0.002 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 6125) covalent geometry : angle 0.53223 / 0.28 ( 8410) hydrogen bonds : bond 0.03970 / 2.67 ( 254) hydrogen bonds : angle 4.42823 / 3.26 ( 721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7557 (mmt180) REVERT: A 352 ASP cc_start: 0.8272 (p0) cc_final: 0.7903 (p0) REVERT: A 388 ASP cc_start: 0.7134 (t70) cc_final: 0.6813 (t0) outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.1845 time to fit residues: 21.6136 Evaluate side-chains 97 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1185 ASN Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.183055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.164747 restraints weight = 30202.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.169756 restraints weight = 14533.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.172860 restraints weight = 8362.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.174880 restraints weight = 5439.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.176241 restraints weight = 3875.417| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6125 Z= 0.164 Angle : 0.540 5.917 8410 Z= 0.287 Chirality : 0.039 0.146 974 Planarity : 0.004 0.037 963 Dihedral : 15.131 107.767 1112 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.16 % Allowed : 20.93 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.33), residues: 654 helix: 1.39 (0.29), residues: 291 sheet: 0.02 (0.64), residues: 76 loop : -0.80 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 399 TYR 0.012 0.002 TYR A 626 PHE 0.011 0.002 PHE A1244 TRP 0.008 0.002 TRP A 509 HIS 0.006 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 6125) covalent geometry : angle 0.53981 / 0.29 ( 8410) hydrogen bonds : bond 0.03947 / 2.65 ( 254) hydrogen bonds : angle 4.45425 / 3.27 ( 721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7743 (mtt180) REVERT: A 337 ARG cc_start: 0.6899 (ttm170) cc_final: 0.6622 (ttp-170) REVERT: A 388 ASP cc_start: 0.7077 (t70) cc_final: 0.6768 (t0) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.2041 time to fit residues: 23.5438 Evaluate side-chains 94 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1185 ASN Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 65 optimal weight: 0.0050 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.183747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.165347 restraints weight = 30648.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.170361 restraints weight = 14707.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.173565 restraints weight = 8458.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.175593 restraints weight = 5452.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.176939 restraints weight = 3875.239| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6125 Z= 0.129 Angle : 0.512 5.395 8410 Z= 0.271 Chirality : 0.038 0.145 974 Planarity : 0.004 0.031 963 Dihedral : 15.090 106.798 1112 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.99 % Allowed : 20.93 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.33), residues: 654 helix: 1.51 (0.29), residues: 291 sheet: 0.04 (0.64), residues: 76 loop : -0.78 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1165 TYR 0.009 0.002 TYR A1173 PHE 0.015 0.001 PHE A1244 TRP 0.010 0.002 TRP A 509 HIS 0.006 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6125) covalent geometry : angle 0.51179 / 0.27 ( 8410) hydrogen bonds : bond 0.03717 / 2.51 ( 254) hydrogen bonds : angle 4.37199 / 3.22 ( 721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 363 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue SER 490 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7725 (mtt180) REVERT: A 337 ARG cc_start: 0.6845 (ttm170) cc_final: 0.6583 (ttp-170) REVERT: A 388 ASP cc_start: 0.7054 (t70) cc_final: 0.6745 (t0) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.1832 time to fit residues: 21.2186 Evaluate side-chains 95 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1008 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1185 ASN Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 68 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.184379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.166078 restraints weight = 30478.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.171143 restraints weight = 14717.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.174277 restraints weight = 8434.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.176310 restraints weight = 5474.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.177591 restraints weight = 3894.044| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6125 Z= 0.120 Angle : 0.506 5.474 8410 Z= 0.266 Chirality : 0.038 0.146 974 Planarity : 0.004 0.032 963 Dihedral : 15.041 105.531 1112 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.83 % Allowed : 21.10 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.33), residues: 654 helix: 1.63 (0.30), residues: 290 sheet: 0.17 (0.65), residues: 76 loop : -0.77 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1165 TYR 0.009 0.001 TYR A1173 PHE 0.011 0.001 PHE A1032 TRP 0.012 0.002 TRP A 509 HIS 0.005 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 6125) covalent geometry : angle 0.50589 / 0.27 ( 8410) hydrogen bonds : bond 0.03485 / 2.37 ( 254) hydrogen bonds : angle 4.28496 / 3.16 ( 721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.33 seconds wall clock time: 35 minutes 53.53 seconds (2153.53 seconds total)