Starting phenix.real_space_refine on Thu Aug 6 05:39:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opp_17084/08_2026/8opp_17084_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opp_17084/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8opp_17084/08_2026/8opp_17084_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opp_17084/08_2026/8opp_17084_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8opp_17084/08_2026/8opp_17084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opp_17084/08_2026/8opp_17084.map" } 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-2.2rc3-6140/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: 2.67, per 1000 atoms: 0.23 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: 1.07 Conformation dependent library (CDL) restraints added in 382.0 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: 1.87 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: 2.54 Time building geometry restraints manager: 1.45 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: 21346 2.55 - 5.09: 101 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=" O5' U D 6 " pdb=" C5' U D 6 " pdb=" C4' U D 6 " ideal model delta sigma weight residual 109.40 112.13 -2.73 8.00e-01 1.56e+00 1.17e+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 ... (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: 2.520 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- 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= 0.341 Angle : 0.653 12.727 8410 Z= 0.328 Chirality : 0.047 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 0.00692 / 0.34 ( 6125) covalent geometry : angle 0.65286 / 0.33 ( 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 : 0.308 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: 0.2148 time to fit residues: 21.7780 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 : 0.296 ------------------------------------------------------------------------------- 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: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4614 r_free = 0.4614 target = 0.190510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.172664 restraints weight = 31076.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.177631 restraints weight = 14650.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.180761 restraints weight = 8305.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.182829 restraints weight = 5329.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.183970 restraints weight = 3736.341| |-----------------------------------------------------------------------------| r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6125 Z= 0.152 Angle : 0.513 5.484 8410 Z= 0.261 Chirality : 0.039 0.188 974 Planarity : 0.004 0.064 963 Dihedral : 15.288 91.807 1112 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.50 % Allowed : 18.60 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.43 (0.33), residues: 654 helix: 2.30 (0.30), residues: 290 sheet: 0.55 (0.63), residues: 76 loop : -0.33 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 583 TYR 0.011 0.001 TYR A1245 PHE 0.013 0.001 PHE A1110 TRP 0.005 0.001 TRP A 555 HIS 0.006 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 6125) covalent geometry : angle 0.51350 / 0.26 ( 8410) hydrogen bonds : bond 0.04376 / 3.04 ( 254) hydrogen bonds : angle 4.29331 / 3.18 ( 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 88 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.270 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: 0.5389 (OUTLIER) cc_final: 0.5035 (mt) outliers start: 9 outliers final: 8 residues processed: 82 average time/residue: 0.1818 time to fit residues: 19.2583 Evaluate side-chains 85 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.190081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.171990 restraints weight = 31314.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.177113 restraints weight = 14927.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.180316 restraints weight = 8403.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.182386 restraints weight = 5362.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.183573 restraints weight = 3767.786| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6125 Z= 0.109 Angle : 0.460 4.355 8410 Z= 0.234 Chirality : 0.037 0.146 974 Planarity : 0.003 0.041 963 Dihedral : 15.188 92.259 1112 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.62 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: 1.35 (0.33), residues: 654 helix: 2.25 (0.30), residues: 290 sheet: 0.51 (0.64), residues: 76 loop : -0.39 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 399 TYR 0.008 0.001 TYR A1173 PHE 0.009 0.001 PHE A 615 TRP 0.006 0.001 TRP A 443 HIS 0.002 0.001 HIS A1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6125) covalent geometry : angle 0.45963 / 0.23 ( 8410) hydrogen bonds : bond 0.03897 / 2.70 ( 254) hydrogen bonds : angle 4.19070 / 3.12 ( 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 90 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.292 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: 0.5407 (OUTLIER) cc_final: 0.5064 (mt) REVERT: A 977 ASP cc_start: 0.6461 (p0) cc_final: 0.6153 (p0) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.1912 time to fit residues: 21.0518 Evaluate side-chains 88 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 446 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 994 THR Chi-restraints excluded: chain A residue 1064 THR 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: 0.7980 chunk 35 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN A1285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.187994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.169839 restraints weight = 31057.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.174889 restraints weight = 14890.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.178009 restraints weight = 8476.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.180051 restraints weight = 5462.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.181418 restraints weight = 3868.722| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6125 Z= 0.163 Angle : 0.509 4.498 8410 Z= 0.264 Chirality : 0.038 0.147 974 Planarity : 0.004 0.032 963 Dihedral : 15.169 96.004 1112 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.66 % Allowed : 19.10 % Favored : 79.24 % 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: 1.03 (0.33), residues: 654 helix: 1.92 (0.29), residues: 290 sheet: 0.43 (0.64), residues: 76 loop : -0.52 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.013 0.002 TYR A1245 PHE 0.023 0.002 PHE A1110 TRP 0.006 0.001 TRP A1238 HIS 0.005 0.001 HIS A1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 6125) covalent geometry : angle 0.50930 / 0.26 ( 8410) hydrogen bonds : bond 0.04064 / 2.79 ( 254) hydrogen bonds : angle 4.31655 / 3.21 ( 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 93 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.219 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 446 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.5127 (mt) REVERT: A 977 ASP cc_start: 0.6561 (p0) cc_final: 0.6280 (p0) REVERT: A 1165 ARG cc_start: 0.8104 (mmp80) cc_final: 0.7846 (mmp80) outliers start: 10 outliers final: 9 residues processed: 88 average time/residue: 0.1642 time to fit residues: 18.5211 Evaluate side-chains 91 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 1310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4588 r_free = 0.4588 target = 0.187894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.169979 restraints weight = 30613.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.175014 restraints weight = 14679.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.178108 restraints weight = 8310.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.180087 restraints weight = 5351.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.181237 restraints weight = 3801.864| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6125 Z= 0.121 Angle : 0.480 5.317 8410 Z= 0.248 Chirality : 0.038 0.145 974 Planarity : 0.004 0.047 963 Dihedral : 15.097 96.202 1112 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.16 % Allowed : 19.27 % 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: 1.05 (0.33), residues: 654 helix: 1.91 (0.29), residues: 291 sheet: 0.42 (0.64), residues: 76 loop : -0.48 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 399 TYR 0.009 0.001 TYR A1173 PHE 0.009 0.001 PHE A1032 TRP 0.010 0.002 TRP A1209 HIS 0.003 0.001 HIS A1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6125) covalent geometry : angle 0.47975 / 0.25 ( 8410) hydrogen bonds : bond 0.03699 / 2.52 ( 254) hydrogen bonds : angle 4.25074 / 3.16 ( 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 95 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.245 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 446 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5169 (mt) REVERT: A 977 ASP cc_start: 0.6586 (p0) cc_final: 0.6337 (p0) REVERT: A 1165 ARG cc_start: 0.8065 (mmp80) cc_final: 0.7608 (mmt-90) outliers start: 13 outliers final: 11 residues processed: 88 average time/residue: 0.1707 time to fit residues: 19.1819 Evaluate side-chains 95 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 42 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.186437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.168071 restraints weight = 30675.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.173134 restraints weight = 14744.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.176313 restraints weight = 8461.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.178365 restraints weight = 5451.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.179394 restraints weight = 3863.382| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6125 Z= 0.143 Angle : 0.499 4.892 8410 Z= 0.258 Chirality : 0.038 0.148 974 Planarity : 0.004 0.055 963 Dihedral : 15.050 98.141 1112 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.33 % Allowed : 19.44 % 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: 0.92 (0.33), residues: 654 helix: 1.79 (0.29), residues: 291 sheet: 0.34 (0.64), residues: 76 loop : -0.52 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 399 TYR 0.013 0.002 TYR A1245 PHE 0.010 0.001 PHE A1032 TRP 0.007 0.001 TRP A 443 HIS 0.005 0.001 HIS A1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6125) covalent geometry : angle 0.49928 / 0.26 ( 8410) hydrogen bonds : bond 0.03748 / 2.55 ( 254) hydrogen bonds : angle 4.27952 / 3.18 ( 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 101 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 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 446 LEU cc_start: 0.5564 (OUTLIER) cc_final: 0.5189 (mt) REVERT: A 977 ASP cc_start: 0.6747 (p0) cc_final: 0.6344 (p0) REVERT: A 1165 ARG cc_start: 0.8029 (mmp80) cc_final: 0.7613 (mmt-90) outliers start: 14 outliers final: 10 residues processed: 95 average time/residue: 0.1972 time to fit residues: 24.2368 Evaluate side-chains 95 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4560 r_free = 0.4560 target = 0.185725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.167304 restraints weight = 30600.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.172348 restraints weight = 14768.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.175486 restraints weight = 8473.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.177542 restraints weight = 5513.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.178835 restraints weight = 3917.692| |-----------------------------------------------------------------------------| r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.2055 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= 0.149 Angle : 0.513 4.927 8410 Z= 0.265 Chirality : 0.039 0.146 974 Planarity : 0.004 0.059 963 Dihedral : 15.042 99.844 1112 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: 0.83 (0.33), residues: 654 helix: 1.73 (0.29), residues: 291 sheet: 0.31 (0.64), residues: 76 loop : -0.59 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 399 TYR 0.011 0.002 TYR A1245 PHE 0.011 0.002 PHE A1244 TRP 0.007 0.002 TRP A 443 HIS 0.005 0.001 HIS A1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6125) covalent geometry : angle 0.51300 / 0.27 ( 8410) hydrogen bonds : bond 0.03789 / 2.57 ( 254) hydrogen bonds : angle 4.30846 / 3.19 ( 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 99 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.187 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 388 ASP cc_start: 0.7047 (t70) cc_final: 0.6749 (t0) REVERT: A 446 LEU cc_start: 0.5573 (OUTLIER) cc_final: 0.5200 (mt) REVERT: A 977 ASP cc_start: 0.6664 (p0) cc_final: 0.6357 (p0) REVERT: A 1165 ARG cc_start: 0.8025 (mmp80) cc_final: 0.7644 (mmt-90) outliers start: 12 outliers final: 11 residues processed: 92 average time/residue: 0.2015 time to fit residues: 23.7288 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 : 0.312 ------------------------------------------------------------------------------- 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 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 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: 0.1980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.0050 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.4569 r_free = 0.4569 target = 0.186492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.168169 restraints weight = 30566.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.173164 restraints weight = 14729.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.176292 restraints weight = 8473.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.178382 restraints weight = 5517.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.179743 restraints weight = 3888.825| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6125 Z= 0.113 Angle : 0.491 5.959 8410 Z= 0.254 Chirality : 0.038 0.147 974 Planarity : 0.004 0.066 963 Dihedral : 14.985 99.265 1112 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.83 % Allowed : 20.76 % 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: 0.98 (0.33), residues: 654 helix: 1.87 (0.30), residues: 291 sheet: 0.35 (0.64), residues: 76 loop : -0.52 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 399 TYR 0.008 0.001 TYR A1173 PHE 0.010 0.001 PHE A1032 TRP 0.009 0.001 TRP A 509 HIS 0.003 0.001 HIS A1090 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 6125) covalent geometry : angle 0.49140 / 0.25 ( 8410) hydrogen bonds : bond 0.03501 / 2.39 ( 254) hydrogen bonds : angle 4.23463 / 3.14 ( 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 97 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.282 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 388 ASP cc_start: 0.7032 (t70) cc_final: 0.6743 (t0) REVERT: A 446 LEU cc_start: 0.5555 (OUTLIER) cc_final: 0.5183 (mt) REVERT: A 604 ASN cc_start: 0.6150 (t0) cc_final: 0.5931 (t0) REVERT: A 977 ASP cc_start: 0.6554 (p0) cc_final: 0.6089 (p0) REVERT: A 1165 ARG cc_start: 0.8007 (mmp80) cc_final: 0.7636 (mmt-90) outliers start: 11 outliers final: 9 residues processed: 90 average time/residue: 0.2205 time to fit residues: 25.2785 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 : 0.314 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 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 = 0.4563 r_free = 0.4563 target = 0.185952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.167688 restraints weight = 30239.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.172741 restraints weight = 14526.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.175855 restraints weight = 8278.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.177861 restraints weight = 5366.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.179204 restraints weight = 3850.410| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6125 Z= 0.130 Angle : 0.502 5.003 8410 Z= 0.259 Chirality : 0.038 0.147 974 Planarity : 0.004 0.068 963 Dihedral : 14.976 99.976 1112 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.66 % Allowed : 21.76 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.92 (0.33), residues: 654 helix: 1.83 (0.29), residues: 291 sheet: 0.33 (0.64), residues: 76 loop : -0.57 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 399 TYR 0.010 0.001 TYR A1245 PHE 0.014 0.001 PHE A1244 TRP 0.008 0.001 TRP A 509 HIS 0.004 0.001 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6125) covalent geometry : angle 0.50215 / 0.26 ( 8410) hydrogen bonds : bond 0.03540 / 2.41 ( 254) hydrogen bonds : angle 4.24152 / 3.14 ( 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 95 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.242 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 388 ASP cc_start: 0.7050 (t70) cc_final: 0.6772 (t0) REVERT: A 604 ASN cc_start: 0.6198 (t0) cc_final: 0.5950 (t0) REVERT: A 977 ASP cc_start: 0.6430 (p0) cc_final: 0.6026 (p0) REVERT: A 1165 ARG cc_start: 0.8016 (mmp80) cc_final: 0.7649 (mmt-90) outliers start: 10 outliers final: 10 residues processed: 89 average time/residue: 0.2191 time to fit residues: 24.6113 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 : 0.304 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4554 r_free = 0.4554 target = 0.185345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.166917 restraints weight = 30750.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.172012 restraints weight = 14758.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.175187 restraints weight = 8425.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.177222 restraints weight = 5441.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.178599 restraints weight = 3874.246| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6125 Z= 0.135 Angle : 0.509 5.287 8410 Z= 0.264 Chirality : 0.038 0.145 974 Planarity : 0.005 0.077 963 Dihedral : 14.982 101.472 1112 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.66 % Allowed : 22.09 % Favored : 76.25 % 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: 0.83 (0.33), residues: 654 helix: 1.75 (0.29), residues: 292 sheet: 0.32 (0.64), residues: 76 loop : -0.63 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 399 TYR 0.009 0.002 TYR A 626 PHE 0.010 0.001 PHE A1032 TRP 0.008 0.001 TRP A 509 HIS 0.004 0.001 HIS A1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6125) covalent geometry : angle 0.50930 / 0.26 ( 8410) hydrogen bonds : bond 0.03599 / 2.45 ( 254) hydrogen bonds : angle 4.26165 / 3.16 ( 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 95 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.296 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 388 ASP cc_start: 0.7065 (t70) cc_final: 0.6774 (t0) REVERT: A 977 ASP cc_start: 0.6318 (p0) cc_final: 0.5985 (p0) REVERT: A 1165 ARG cc_start: 0.8009 (mmp80) cc_final: 0.7741 (mmt-90) outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.2069 time to fit residues: 23.1640 Evaluate side-chains 91 residues out of total 611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 0.0020 chunk 7 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.184690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.166343 restraints weight = 30448.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.171397 restraints weight = 14739.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.174508 restraints weight = 8445.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.176573 restraints weight = 5504.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.177942 restraints weight = 3922.146| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6125 Z= 0.136 Angle : 0.510 5.333 8410 Z= 0.265 Chirality : 0.038 0.145 974 Planarity : 0.004 0.070 963 Dihedral : 14.994 102.908 1112 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.66 % Allowed : 22.26 % Favored : 76.08 % 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: 0.80 (0.33), residues: 654 helix: 1.73 (0.29), residues: 292 sheet: 0.34 (0.65), residues: 76 loop : -0.66 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 399 TYR 0.010 0.002 TYR A1245 PHE 0.010 0.001 PHE A1032 TRP 0.008 0.002 TRP A 509 HIS 0.004 0.001 HIS A1286 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6125) covalent geometry : angle 0.51045 / 0.27 ( 8410) hydrogen bonds : bond 0.03588 / 2.44 ( 254) hydrogen bonds : angle 4.26140 / 3.15 ( 721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2209.07 seconds wall clock time: 38 minutes 20.89 seconds (2300.89 seconds total)