Starting phenix.real_space_refine on Sat May 2 13:54:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vrc_65283/05_2026/9vrc_65283.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vrc_65283/05_2026/9vrc_65283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vrc_65283/05_2026/9vrc_65283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vrc_65283/05_2026/9vrc_65283.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vrc_65283/05_2026/9vrc_65283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vrc_65283/05_2026/9vrc_65283.map" } resolution = 3.21 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= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 3872 2.51 5 N 996 2.21 5 O 1063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5965 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 5965 Classifications: {'peptide': 756} Link IDs: {'PTRANS': 28, 'TRANS': 727} Chain breaks: 6 Time building chain proxies: 1.62, per 1000 atoms: 0.27 Number of scatterers: 5965 At special positions: 0 Unit cell: (133.488, 73.336, 99.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1063 8.00 N 996 7.00 C 3872 6.00 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: 0.49 Conformation dependent library (CDL) restraints added in 337.7 milliseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1426 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 2 sheets defined 74.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 305 through 338 removed outlier: 4.230A pdb=" N GLY A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 4.308A pdb=" N SER A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 391 removed outlier: 3.929A pdb=" N LEU A 391 " --> pdb=" O TYR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 421 through 427 removed outlier: 4.730A pdb=" N HIS A 425 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 427 " --> pdb=" O PHE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 494 Proline residue: A 465 - end of helix removed outlier: 3.969A pdb=" N GLU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 504 through 555 removed outlier: 3.946A pdb=" N VAL A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 518 " --> pdb=" O MET A 514 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 540 - end of helix removed outlier: 3.579A pdb=" N GLY A 555 " --> pdb=" O CYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 602 removed outlier: 4.249A pdb=" N ARG A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Proline residue: A 576 - end of helix Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 926 through 935 removed outlier: 4.140A pdb=" N TYR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 940 removed outlier: 4.042A pdb=" N LYS A 939 " --> pdb=" O GLU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 967 removed outlier: 3.548A pdb=" N LEU A 945 " --> pdb=" O THR A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1025 Processing helix chain 'A' and resid 1028 through 1035 removed outlier: 3.569A pdb=" N PHE A1032 " --> pdb=" O PRO A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1053 removed outlier: 3.620A pdb=" N ILE A1040 " --> pdb=" O PRO A1036 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1080 Processing helix chain 'A' and resid 1166 through 1188 Processing helix chain 'A' and resid 1195 through 1207 Processing helix chain 'A' and resid 1208 through 1227 Processing helix chain 'A' and resid 1227 through 1237 Processing helix chain 'A' and resid 1301 through 1310 removed outlier: 4.117A pdb=" N ILE A1306 " --> pdb=" O LYS A1302 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1337 Processing helix chain 'A' and resid 1352 through 1358 Processing helix chain 'A' and resid 1364 through 1375 Processing helix chain 'A' and resid 1377 through 1384 removed outlier: 3.544A pdb=" N SER A1383 " --> pdb=" O GLU A1379 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A1384 " --> pdb=" O VAL A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.714A pdb=" N GLN A1405 " --> pdb=" O VAL A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1445 Processing helix chain 'A' and resid 1457 through 1461 Processing sheet with id=AA1, first strand: chain 'A' and resid 1262 through 1266 removed outlier: 3.704A pdb=" N VAL A1265 " --> pdb=" O LYS A1319 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS A1319 " --> pdb=" O VAL A1265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1340 through 1342 removed outlier: 3.503A pdb=" N SER A1340 " --> pdb=" O ILE A1419 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A1420 " --> pdb=" O CYS A1451 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A1453 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A1422 " --> pdb=" O ILE A1453 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS A1291 " --> pdb=" O LEU A1465 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A1467 " --> pdb=" O LYS A1291 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY A1293 " --> pdb=" O LEU A1467 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU A1469 " --> pdb=" O GLY A1293 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A1468 " --> pdb=" O ALA A1475 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1880 1.34 - 1.46: 1034 1.46 - 1.58: 3115 1.58 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 6084 Sorted by residual: bond pdb=" CA LYS A1078 " pdb=" C LYS A1078 " ideal model delta sigma weight residual 1.524 1.504 0.021 1.24e-02 6.50e+03 2.76e+00 bond pdb=" CA CYS A1284 " pdb=" C CYS A1284 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.18e-02 7.18e+03 2.59e+00 bond pdb=" CA ARG A 523 " pdb=" C ARG A 523 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.24e-02 6.50e+03 2.56e+00 bond pdb=" CA LYS A1019 " pdb=" C LYS A1019 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.27e-02 6.20e+03 2.23e+00 bond pdb=" CB GLN A1481 " pdb=" CG GLN A1481 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.20e+00 ... (remaining 6079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 7712 1.16 - 2.31: 422 2.31 - 3.47: 84 3.47 - 4.63: 26 4.63 - 5.79: 6 Bond angle restraints: 8250 Sorted by residual: angle pdb=" CB GLN A1481 " pdb=" CG GLN A1481 " pdb=" CD GLN A1481 " ideal model delta sigma weight residual 112.60 118.07 -5.47 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N LYS A 389 " pdb=" CA LYS A 389 " pdb=" C LYS A 389 " ideal model delta sigma weight residual 113.50 109.95 3.55 1.23e+00 6.61e-01 8.33e+00 angle pdb=" N ARG A1058 " pdb=" CA ARG A1058 " pdb=" C ARG A1058 " ideal model delta sigma weight residual 111.36 108.49 2.87 1.09e+00 8.42e-01 6.93e+00 angle pdb=" N CYS A1284 " pdb=" CA CYS A1284 " pdb=" C CYS A1284 " ideal model delta sigma weight residual 109.95 113.96 -4.01 1.59e+00 3.96e-01 6.35e+00 angle pdb=" CA GLN A1481 " pdb=" CB GLN A1481 " pdb=" CG GLN A1481 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.10e+00 ... (remaining 8245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3224 17.93 - 35.85: 348 35.85 - 53.78: 60 53.78 - 71.70: 10 71.70 - 89.63: 1 Dihedral angle restraints: 3643 sinusoidal: 1447 harmonic: 2196 Sorted by residual: dihedral pdb=" CA ASN A1356 " pdb=" CB ASN A1356 " pdb=" CG ASN A1356 " pdb=" OD1 ASN A1356 " ideal model delta sinusoidal sigma weight residual 120.00 -168.71 -71.29 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA LEU A1053 " pdb=" C LEU A1053 " pdb=" N ASP A1054 " pdb=" CA ASP A1054 " ideal model delta harmonic sigma weight residual 180.00 -163.99 -16.01 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CG ARG A1411 " pdb=" CD ARG A1411 " pdb=" NE ARG A1411 " pdb=" CZ ARG A1411 " ideal model delta sinusoidal sigma weight residual 180.00 136.45 43.55 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 3640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 684 0.033 - 0.067: 215 0.067 - 0.100: 51 0.100 - 0.133: 19 0.133 - 0.166: 4 Chirality restraints: 973 Sorted by residual: chirality pdb=" CA ILE A1419 " pdb=" N ILE A1419 " pdb=" C ILE A1419 " pdb=" CB ILE A1419 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE A1262 " pdb=" N ILE A1262 " pdb=" C ILE A1262 " pdb=" CB ILE A1262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE A1474 " pdb=" N ILE A1474 " pdb=" C ILE A1474 " pdb=" CB ILE A1474 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 970 not shown) Planarity restraints: 1019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 955 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C VAL A 955 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL A 955 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 956 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 954 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C GLN A 954 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN A 954 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 955 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 953 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C PHE A 953 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE A 953 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN A 954 " 0.010 2.00e-02 2.50e+03 ... (remaining 1016 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 3392 2.99 - 3.47: 6745 3.47 - 3.94: 9544 3.94 - 4.42: 11273 4.42 - 4.90: 17381 Nonbonded interactions: 48335 Sorted by model distance: nonbonded pdb=" OG1 THR A 452 " pdb=" OG1 THR A 547 " model vdw 2.510 3.040 nonbonded pdb=" O GLN A1048 " pdb=" OD2 ASP A1052 " model vdw 2.535 3.040 nonbonded pdb=" O GLY A1301 " pdb=" OG1 THR A1304 " model vdw 2.547 3.040 nonbonded pdb=" O GLU A1362 " pdb=" OE1 GLU A1362 " model vdw 2.552 3.040 nonbonded pdb=" O VAL A1265 " pdb=" OD1 ASP A1266 " model vdw 2.553 3.040 ... (remaining 48330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.360 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.004 0.045 6084 Z= 0.234 Angle : 0.645 5.785 8250 Z= 0.376 Chirality : 0.037 0.166 973 Planarity : 0.004 0.025 1019 Dihedral : 14.378 89.625 2217 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.76 % Allowed : 15.44 % Favored : 83.79 % 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: 1.59 (0.31), residues: 742 helix: 1.38 (0.23), residues: 534 sheet: -0.23 (1.14), residues: 25 loop : 0.55 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 571 TYR 0.009 0.001 TYR A 420 PHE 0.010 0.001 PHE A1017 TRP 0.005 0.001 TRP A1166 HIS 0.001 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 6084) covalent geometry : angle 0.64464 ( 8250) hydrogen bonds : bond 0.14722 ( 424) hydrogen bonds : angle 6.62335 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 TRP cc_start: 0.5497 (t-100) cc_final: 0.5101 (m-10) REVERT: A 302 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7555 (mptt) REVERT: A 574 GLN cc_start: 0.8799 (pp30) cc_final: 0.8514 (pp30) REVERT: A 1471 ASP cc_start: 0.7782 (m-30) cc_final: 0.7564 (t0) outliers start: 5 outliers final: 2 residues processed: 114 average time/residue: 0.1264 time to fit residues: 17.0731 Evaluate side-chains 99 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 964 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.084951 restraints weight = 12206.474| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.74 r_work: 0.3087 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6084 Z= 0.135 Angle : 0.515 6.012 8250 Z= 0.261 Chirality : 0.038 0.153 973 Planarity : 0.003 0.033 1019 Dihedral : 3.946 38.587 820 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.45 % Allowed : 14.68 % Favored : 82.87 % 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: 2.88 (0.31), residues: 742 helix: 2.45 (0.22), residues: 541 sheet: 0.03 (1.18), residues: 25 loop : 0.56 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1329 TYR 0.011 0.001 TYR A1271 PHE 0.015 0.001 PHE A1477 TRP 0.007 0.001 TRP A 305 HIS 0.001 0.000 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6084) covalent geometry : angle 0.51480 ( 8250) hydrogen bonds : bond 0.04666 ( 424) hydrogen bonds : angle 4.18195 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7630 (mptt) REVERT: A 426 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8492 (t0) REVERT: A 539 SER cc_start: 0.9378 (m) cc_final: 0.9113 (p) REVERT: A 574 GLN cc_start: 0.8814 (pp30) cc_final: 0.8561 (pp30) REVERT: A 1471 ASP cc_start: 0.8324 (m-30) cc_final: 0.7883 (t0) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.1057 time to fit residues: 13.3782 Evaluate side-chains 100 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain A residue 1221 CYS Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1390 SER Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.108092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085579 restraints weight = 12142.894| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.73 r_work: 0.3106 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6084 Z= 0.113 Angle : 0.464 5.472 8250 Z= 0.236 Chirality : 0.037 0.129 973 Planarity : 0.003 0.031 1019 Dihedral : 3.516 35.938 816 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.36 % Allowed : 15.90 % Favored : 80.73 % 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: 3.19 (0.31), residues: 742 helix: 2.78 (0.22), residues: 539 sheet: 0.17 (1.17), residues: 25 loop : 0.28 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1329 TYR 0.009 0.001 TYR A 420 PHE 0.011 0.001 PHE A 314 TRP 0.006 0.001 TRP A 962 HIS 0.002 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6084) covalent geometry : angle 0.46357 ( 8250) hydrogen bonds : bond 0.04156 ( 424) hydrogen bonds : angle 3.79558 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 302 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7651 (mttp) REVERT: A 359 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8561 (mp) REVERT: A 426 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8361 (t0) REVERT: A 539 SER cc_start: 0.9347 (m) cc_final: 0.9094 (p) REVERT: A 1207 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8832 (mm) REVERT: A 1354 ARG cc_start: 0.8225 (ttt-90) cc_final: 0.7878 (tpt170) REVERT: A 1471 ASP cc_start: 0.8259 (m-30) cc_final: 0.7876 (t0) REVERT: A 1481 GLN cc_start: 0.8163 (mp10) cc_final: 0.7941 (mp10) outliers start: 22 outliers final: 13 residues processed: 110 average time/residue: 0.1010 time to fit residues: 13.9270 Evaluate side-chains 109 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1215 ARG Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1390 SER Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 494 ASN ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.106968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084644 restraints weight = 12230.457| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.74 r_work: 0.3092 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6084 Z= 0.125 Angle : 0.479 5.913 8250 Z= 0.243 Chirality : 0.037 0.167 973 Planarity : 0.003 0.032 1019 Dihedral : 3.577 36.695 816 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.75 % Allowed : 17.13 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.26 (0.31), residues: 742 helix: 2.85 (0.22), residues: 541 sheet: 0.13 (1.15), residues: 25 loop : 0.21 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1329 TYR 0.009 0.001 TYR A 420 PHE 0.013 0.001 PHE A 342 TRP 0.006 0.001 TRP A 962 HIS 0.001 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6084) covalent geometry : angle 0.47898 ( 8250) hydrogen bonds : bond 0.04029 ( 424) hydrogen bonds : angle 3.69532 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 302 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7699 (mttp) REVERT: A 359 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8585 (mp) REVERT: A 539 SER cc_start: 0.9357 (m) cc_final: 0.9126 (p) REVERT: A 574 GLN cc_start: 0.8826 (pp30) cc_final: 0.8526 (pp30) REVERT: A 1207 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8812 (mm) REVERT: A 1268 LYS cc_start: 0.8999 (mttt) cc_final: 0.8600 (mmtm) REVERT: A 1354 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7952 (tpt170) REVERT: A 1471 ASP cc_start: 0.8243 (m-30) cc_final: 0.7878 (t0) REVERT: A 1481 GLN cc_start: 0.8224 (mp10) cc_final: 0.7990 (mp10) outliers start: 18 outliers final: 14 residues processed: 108 average time/residue: 0.1036 time to fit residues: 13.9105 Evaluate side-chains 112 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1226 ARG Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084198 restraints weight = 12424.537| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.77 r_work: 0.3086 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6084 Z= 0.132 Angle : 0.480 5.664 8250 Z= 0.242 Chirality : 0.037 0.127 973 Planarity : 0.003 0.042 1019 Dihedral : 3.541 36.711 816 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.06 % Allowed : 17.28 % Favored : 79.66 % 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: 3.32 (0.31), residues: 742 helix: 2.93 (0.22), residues: 541 sheet: -0.12 (1.12), residues: 25 loop : 0.14 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1329 TYR 0.009 0.001 TYR A 420 PHE 0.024 0.001 PHE A1181 TRP 0.023 0.001 TRP A1166 HIS 0.002 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6084) covalent geometry : angle 0.48049 ( 8250) hydrogen bonds : bond 0.03993 ( 424) hydrogen bonds : angle 3.63833 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.245 Fit side-chains REVERT: A 302 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7785 (mttp) REVERT: A 359 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8596 (mp) REVERT: A 367 TRP cc_start: 0.8622 (t60) cc_final: 0.8286 (t60) REVERT: A 539 SER cc_start: 0.9363 (m) cc_final: 0.9140 (p) REVERT: A 574 GLN cc_start: 0.8866 (pp30) cc_final: 0.8600 (pp30) REVERT: A 1207 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8822 (mm) REVERT: A 1268 LYS cc_start: 0.8984 (mttt) cc_final: 0.8558 (mmtm) REVERT: A 1271 TYR cc_start: 0.7773 (m-80) cc_final: 0.7371 (m-80) REVERT: A 1354 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.7928 (tpt170) REVERT: A 1471 ASP cc_start: 0.8254 (m-30) cc_final: 0.7877 (t0) outliers start: 20 outliers final: 14 residues processed: 105 average time/residue: 0.1061 time to fit residues: 13.9221 Evaluate side-chains 105 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084131 restraints weight = 12199.418| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.71 r_work: 0.3080 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6084 Z= 0.132 Angle : 0.489 7.464 8250 Z= 0.245 Chirality : 0.037 0.122 973 Planarity : 0.003 0.042 1019 Dihedral : 3.534 36.401 816 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.06 % Allowed : 18.20 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.38 (0.31), residues: 742 helix: 2.99 (0.21), residues: 541 sheet: -0.22 (1.12), residues: 25 loop : 0.15 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1329 TYR 0.009 0.001 TYR A 420 PHE 0.015 0.001 PHE A 342 TRP 0.017 0.001 TRP A1166 HIS 0.001 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6084) covalent geometry : angle 0.48861 ( 8250) hydrogen bonds : bond 0.03943 ( 424) hydrogen bonds : angle 3.60912 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 302 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7790 (mttp) REVERT: A 359 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8581 (mp) REVERT: A 367 TRP cc_start: 0.8643 (t60) cc_final: 0.8338 (t60) REVERT: A 539 SER cc_start: 0.9359 (m) cc_final: 0.9138 (p) REVERT: A 571 ARG cc_start: 0.8827 (tmt170) cc_final: 0.8587 (tmm-80) REVERT: A 1207 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8831 (mm) REVERT: A 1222 LYS cc_start: 0.8886 (tptp) cc_final: 0.8652 (tptt) REVERT: A 1285 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8502 (tt) REVERT: A 1354 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.7901 (tpt170) REVERT: A 1471 ASP cc_start: 0.8280 (m-30) cc_final: 0.7901 (t0) REVERT: A 1481 GLN cc_start: 0.8319 (mp10) cc_final: 0.8105 (mp10) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.1050 time to fit residues: 13.4582 Evaluate side-chains 109 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1221 CYS Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A1356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.107695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085464 restraints weight = 12251.426| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.75 r_work: 0.3100 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6084 Z= 0.116 Angle : 0.500 10.382 8250 Z= 0.246 Chirality : 0.037 0.123 973 Planarity : 0.003 0.040 1019 Dihedral : 3.517 35.773 816 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.21 % Allowed : 17.89 % Favored : 78.90 % 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: 3.43 (0.31), residues: 742 helix: 3.02 (0.21), residues: 541 sheet: -0.29 (1.13), residues: 25 loop : 0.20 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1329 TYR 0.008 0.001 TYR A 420 PHE 0.025 0.001 PHE A1181 TRP 0.014 0.001 TRP A1166 HIS 0.001 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6084) covalent geometry : angle 0.49964 ( 8250) hydrogen bonds : bond 0.03801 ( 424) hydrogen bonds : angle 3.52381 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8186 (m-40) REVERT: A 359 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8571 (mp) REVERT: A 367 TRP cc_start: 0.8605 (t60) cc_final: 0.8219 (t60) REVERT: A 539 SER cc_start: 0.9340 (m) cc_final: 0.9123 (p) REVERT: A 571 ARG cc_start: 0.8832 (tmt170) cc_final: 0.8632 (tmm-80) REVERT: A 574 GLN cc_start: 0.8860 (pp30) cc_final: 0.8587 (pp30) REVERT: A 1207 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8833 (mm) REVERT: A 1222 LYS cc_start: 0.8887 (tptp) cc_final: 0.8649 (tptt) REVERT: A 1285 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8525 (tt) REVERT: A 1354 ARG cc_start: 0.8240 (ttt-90) cc_final: 0.7918 (tpt170) REVERT: A 1471 ASP cc_start: 0.8269 (m-30) cc_final: 0.7927 (t0) REVERT: A 1481 GLN cc_start: 0.8347 (mp10) cc_final: 0.8139 (mp10) outliers start: 21 outliers final: 16 residues processed: 106 average time/residue: 0.0948 time to fit residues: 12.7706 Evaluate side-chains 114 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1221 CYS Chi-restraints excluded: chain A residue 1285 ILE Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.106916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084847 restraints weight = 12201.096| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.71 r_work: 0.3095 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6084 Z= 0.128 Angle : 0.506 13.055 8250 Z= 0.246 Chirality : 0.037 0.121 973 Planarity : 0.003 0.032 1019 Dihedral : 3.239 16.675 812 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.06 % Allowed : 17.89 % Favored : 79.05 % 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: 3.45 (0.31), residues: 742 helix: 3.05 (0.21), residues: 541 sheet: -2.04 (1.23), residues: 17 loop : 0.32 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1329 TYR 0.009 0.001 TYR A 420 PHE 0.016 0.001 PHE A 342 TRP 0.011 0.001 TRP A1166 HIS 0.001 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6084) covalent geometry : angle 0.50604 ( 8250) hydrogen bonds : bond 0.03825 ( 424) hydrogen bonds : angle 3.52311 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8291 (m-40) REVERT: A 359 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 367 TRP cc_start: 0.8615 (t60) cc_final: 0.8092 (t60) REVERT: A 539 SER cc_start: 0.9345 (m) cc_final: 0.9128 (p) REVERT: A 574 GLN cc_start: 0.8877 (pp30) cc_final: 0.8621 (pp30) REVERT: A 1207 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8827 (mm) REVERT: A 1222 LYS cc_start: 0.8898 (tptp) cc_final: 0.8657 (tptt) REVERT: A 1354 ARG cc_start: 0.8274 (ttt-90) cc_final: 0.8005 (tpt170) REVERT: A 1471 ASP cc_start: 0.8278 (m-30) cc_final: 0.7956 (t0) REVERT: A 1481 GLN cc_start: 0.8395 (mp10) cc_final: 0.8184 (mp10) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.1015 time to fit residues: 13.1377 Evaluate side-chains 110 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 65 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.108011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085918 restraints weight = 12115.581| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.72 r_work: 0.3105 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6084 Z= 0.115 Angle : 0.526 13.198 8250 Z= 0.254 Chirality : 0.037 0.146 973 Planarity : 0.003 0.031 1019 Dihedral : 3.292 19.226 812 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.29 % Allowed : 19.42 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.47 (0.31), residues: 742 helix: 3.10 (0.21), residues: 541 sheet: -2.21 (1.21), residues: 18 loop : 0.28 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1329 TYR 0.008 0.001 TYR A 420 PHE 0.016 0.001 PHE A 342 TRP 0.011 0.001 TRP A1166 HIS 0.001 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6084) covalent geometry : angle 0.52566 ( 8250) hydrogen bonds : bond 0.03725 ( 424) hydrogen bonds : angle 3.48399 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 359 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8567 (mp) REVERT: A 482 ASP cc_start: 0.8753 (m-30) cc_final: 0.8484 (m-30) REVERT: A 539 SER cc_start: 0.9332 (m) cc_final: 0.9113 (p) REVERT: A 574 GLN cc_start: 0.8876 (pp30) cc_final: 0.8629 (pp30) REVERT: A 1207 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8828 (mm) REVERT: A 1222 LYS cc_start: 0.8901 (tptp) cc_final: 0.8652 (tptt) REVERT: A 1354 ARG cc_start: 0.8257 (ttt-90) cc_final: 0.7983 (tpt170) REVERT: A 1471 ASP cc_start: 0.8289 (m-30) cc_final: 0.7994 (t0) REVERT: A 1481 GLN cc_start: 0.8390 (mp10) cc_final: 0.8185 (mp10) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.1002 time to fit residues: 13.2973 Evaluate side-chains 109 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 66 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.108369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086230 restraints weight = 12180.484| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.75 r_work: 0.3118 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6084 Z= 0.108 Angle : 0.508 13.320 8250 Z= 0.245 Chirality : 0.037 0.122 973 Planarity : 0.003 0.032 1019 Dihedral : 3.240 17.821 812 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.99 % Allowed : 19.72 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.56 (0.31), residues: 742 helix: 3.17 (0.21), residues: 541 sheet: -2.17 (1.20), residues: 18 loop : 0.25 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1329 TYR 0.008 0.001 TYR A 420 PHE 0.024 0.001 PHE A1181 TRP 0.015 0.001 TRP A1166 HIS 0.001 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6084) covalent geometry : angle 0.50807 ( 8250) hydrogen bonds : bond 0.03579 ( 424) hydrogen bonds : angle 3.40782 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.209 Fit side-chains REVERT: A 359 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8558 (mt) REVERT: A 367 TRP cc_start: 0.8593 (t60) cc_final: 0.8231 (t60) REVERT: A 482 ASP cc_start: 0.8761 (m-30) cc_final: 0.8496 (m-30) REVERT: A 539 SER cc_start: 0.9326 (m) cc_final: 0.9106 (p) REVERT: A 574 GLN cc_start: 0.8863 (pp30) cc_final: 0.8615 (pp30) REVERT: A 1207 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 1222 LYS cc_start: 0.8902 (tptp) cc_final: 0.8650 (tptt) REVERT: A 1268 LYS cc_start: 0.8937 (mttt) cc_final: 0.8580 (mmtm) REVERT: A 1354 ARG cc_start: 0.8261 (ttt-90) cc_final: 0.7967 (tpt170) REVERT: A 1471 ASP cc_start: 0.8276 (m-30) cc_final: 0.8015 (t0) REVERT: A 1481 GLN cc_start: 0.8446 (mp10) cc_final: 0.8226 (mp10) outliers start: 13 outliers final: 11 residues processed: 105 average time/residue: 0.0947 time to fit residues: 12.6615 Evaluate side-chains 107 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.107762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085747 restraints weight = 12263.521| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.69 r_work: 0.3116 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6084 Z= 0.124 Angle : 0.532 13.147 8250 Z= 0.256 Chirality : 0.037 0.124 973 Planarity : 0.003 0.042 1019 Dihedral : 3.237 17.261 812 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.14 % Allowed : 20.49 % Favored : 77.37 % 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: 3.57 (0.31), residues: 742 helix: 3.18 (0.21), residues: 541 sheet: -1.82 (1.26), residues: 17 loop : 0.22 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1329 TYR 0.008 0.001 TYR A 420 PHE 0.015 0.001 PHE A 342 TRP 0.015 0.001 TRP A1166 HIS 0.001 0.000 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6084) covalent geometry : angle 0.53240 ( 8250) hydrogen bonds : bond 0.03642 ( 424) hydrogen bonds : angle 3.43896 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1455.04 seconds wall clock time: 25 minutes 43.44 seconds (1543.44 seconds total)