Starting phenix.real_space_refine on Wed Jul 1 23:10:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yho_33832/07_2026/7yho_33832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yho_33832/07_2026/7yho_33832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yho_33832/07_2026/7yho_33832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yho_33832/07_2026/7yho_33832.map" model { file = "/net/cci-nas-00/data/ceres_data/7yho_33832/07_2026/7yho_33832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yho_33832/07_2026/7yho_33832.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yho_33832/07_2026/7yho_33832.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yho_33832/07_2026/7yho_33832.cif" } resolution = 3.3 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= 0.001 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 49 5.49 5 S 23 5.16 5 C 2348 2.51 5 N 697 2.21 5 O 802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3923 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2910 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 22, 'TRANS': 338} Chain breaks: 5 Chain: "B" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 539 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 466 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1826 SG CYS A1045 53.403 54.606 40.943 1.00 78.34 S ATOM 1774 SG CYS A1038 50.038 53.672 46.312 1.00 73.18 S ATOM 1845 SG CYS A1048 55.115 57.801 46.484 1.00 81.69 S ATOM 1888 SG CYS A1054 55.624 51.262 45.560 1.00 83.08 S Time building chain proxies: 1.06, per 1000 atoms: 0.27 Number of scatterers: 3923 At special positions: 0 Unit cell: (73.03, 105.19, 89.11, 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) Fe 4 26.01 S 23 16.00 P 49 15.00 O 802 8.00 N 697 7.00 C 2348 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: 0.30 Conformation dependent library (CDL) restraints added in 107.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A1054 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A1048 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A1045 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A1038 " Number of angles added : 12 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 59.0% alpha, 6.9% beta 19 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.603A pdb=" N GLU A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 606 Processing helix chain 'A' and resid 610 through 625 Processing helix chain 'A' and resid 884 through 891 Processing helix chain 'A' and resid 892 through 900 removed outlier: 3.659A pdb=" N VAL A 896 " --> pdb=" O ASP A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 923 Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 936 through 947 removed outlier: 3.948A pdb=" N PHE A 947 " --> pdb=" O TYR A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 962 Processing helix chain 'A' and resid 971 through 981 Processing helix chain 'A' and resid 1007 through 1016 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1019 through 1037 Processing helix chain 'A' and resid 1048 through 1052 removed outlier: 4.242A pdb=" N GLY A1052 " --> pdb=" O PRO A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1061 removed outlier: 3.637A pdb=" N ALA A1058 " --> pdb=" O CYS A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1217 removed outlier: 4.438A pdb=" N GLN A1217 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1291 Processing helix chain 'A' and resid 1295 through 1299 Processing helix chain 'A' and resid 1309 through 1315 Processing helix chain 'A' and resid 1337 through 1342 removed outlier: 3.823A pdb=" N ILE A1341 " --> pdb=" O SER A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1356 removed outlier: 3.866A pdb=" N ILE A1350 " --> pdb=" O SER A1346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1204 through 1207 removed outlier: 4.006A pdb=" N TYR A1206 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR A1358 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A1331 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS A1360 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR A1333 " --> pdb=" O CYS A1360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1363 through 1364 removed outlier: 3.757A pdb=" N GLY A1363 " --> pdb=" O LYS A1372 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 369 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 1676 1.41 - 1.63: 2406 1.63 - 1.84: 30 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 4124 Sorted by residual: bond pdb=" CA LEU A1026 " pdb=" C LEU A1026 " ideal model delta sigma weight residual 1.523 1.432 0.092 1.30e-02 5.92e+03 4.97e+01 bond pdb=" CA HIS A1027 " pdb=" C HIS A1027 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.39e-02 5.18e+03 3.25e+01 bond pdb=" C THR A1022 " pdb=" O THR A1022 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.90e+01 bond pdb=" N TYR A1028 " pdb=" CA TYR A1028 " ideal model delta sigma weight residual 1.459 1.407 0.053 1.21e-02 6.83e+03 1.89e+01 bond pdb=" CA HIS A1027 " pdb=" CB HIS A1027 " ideal model delta sigma weight residual 1.530 1.457 0.073 1.68e-02 3.54e+03 1.87e+01 ... (remaining 4119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 5693 2.52 - 5.04: 89 5.04 - 7.56: 9 7.56 - 10.08: 2 10.08 - 12.59: 3 Bond angle restraints: 5796 Sorted by residual: angle pdb=" N TYR A1028 " pdb=" CA TYR A1028 " pdb=" C TYR A1028 " ideal model delta sigma weight residual 111.28 98.69 12.59 1.09e+00 8.42e-01 1.34e+02 angle pdb=" N HIS A1027 " pdb=" CA HIS A1027 " pdb=" C HIS A1027 " ideal model delta sigma weight residual 112.89 123.53 -10.64 1.24e+00 6.50e-01 7.36e+01 angle pdb=" N ILE A1031 " pdb=" CA ILE A1031 " pdb=" C ILE A1031 " ideal model delta sigma weight residual 110.62 103.40 7.22 1.02e+00 9.61e-01 5.00e+01 angle pdb=" N LEU A1026 " pdb=" CA LEU A1026 " pdb=" C LEU A1026 " ideal model delta sigma weight residual 111.28 103.77 7.51 1.09e+00 8.42e-01 4.74e+01 angle pdb=" CB HIS A1027 " pdb=" CG HIS A1027 " pdb=" CD2 HIS A1027 " ideal model delta sigma weight residual 131.20 123.55 7.65 1.30e+00 5.92e-01 3.46e+01 ... (remaining 5791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 2041 35.70 - 71.39: 273 71.39 - 107.09: 2 107.09 - 142.79: 0 142.79 - 178.48: 1 Dihedral angle restraints: 2317 sinusoidal: 1272 harmonic: 1045 Sorted by residual: dihedral pdb=" C HIS A1027 " pdb=" N HIS A1027 " pdb=" CA HIS A1027 " pdb=" CB HIS A1027 " ideal model delta harmonic sigma weight residual -122.60 -143.67 21.07 0 2.50e+00 1.60e-01 7.11e+01 dihedral pdb=" N HIS A1027 " pdb=" C HIS A1027 " pdb=" CA HIS A1027 " pdb=" CB HIS A1027 " ideal model delta harmonic sigma weight residual 122.80 143.77 -20.97 0 2.50e+00 1.60e-01 7.04e+01 dihedral pdb=" C4' DT C 17 " pdb=" C3' DT C 17 " pdb=" O3' DT C 17 " pdb=" P DT C 18 " ideal model delta sinusoidal sigma weight residual 220.00 41.52 178.48 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 2314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 634 0.231 - 0.462: 0 0.462 - 0.693: 2 0.693 - 0.924: 0 0.924 - 1.155: 1 Chirality restraints: 637 Sorted by residual: chirality pdb=" CA HIS A1027 " pdb=" N HIS A1027 " pdb=" C HIS A1027 " pdb=" CB HIS A1027 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" P DG B 6 " pdb=" OP1 DG B 6 " pdb=" OP2 DG B 6 " pdb=" O5' DG B 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" P DG B 3 " pdb=" OP1 DG B 3 " pdb=" OP2 DG B 3 " pdb=" O5' DG B 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.82 -0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 634 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1028 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C TYR A1028 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR A1028 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A1029 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1294 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A1295 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1295 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1295 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1023 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LEU A1023 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU A1023 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A1024 " 0.008 2.00e-02 2.50e+03 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 946 2.80 - 3.32: 3506 3.32 - 3.85: 7076 3.85 - 4.37: 7802 4.37 - 4.90: 12189 Nonbonded interactions: 31519 Sorted by model distance: nonbonded pdb=" NH1 ARG A 566 " pdb=" O PRO A1013 " model vdw 2.273 3.120 nonbonded pdb=" O GLN A 607 " pdb=" NH2 ARG A 903 " model vdw 2.286 3.120 nonbonded pdb=" N HIS A1310 " pdb=" O PHE A1364 " model vdw 2.338 3.120 nonbonded pdb=" NH1 ARG A 572 " pdb=" O GLY A 982 " model vdw 2.374 3.120 nonbonded pdb=" NZ LYS A 908 " pdb=" O2 DC B 14 " model vdw 2.428 3.120 ... (remaining 31514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 : 0.006 0.092 4128 Z= 0.465 Angle : 0.844 12.594 5808 Z= 0.639 Chirality : 0.070 1.155 637 Planarity : 0.004 0.040 561 Dihedral : 23.571 178.481 1637 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 8.78 % Allowed : 12.85 % Favored : 78.37 % Cbeta Deviations : 0.29 % 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: 0.44 (0.45), residues: 349 helix: 1.33 (0.40), residues: 178 sheet: 1.75 (1.40), residues: 12 loop : -1.04 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1204 TYR 0.012 0.001 TYR A1024 PHE 0.019 0.001 PHE A1033 TRP 0.005 0.001 TRP A1012 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.47 ( 4124) covalent geometry : angle 0.80791 / 0.64 ( 5796) hydrogen bonds : bond 0.17597 / 11.78 ( 181) hydrogen bonds : angle 7.33081 / 5.37 ( 465) metal coordination : bond 0.00351 / 0.18 ( 4) metal coordination : angle 5.46808 / 3.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 580 MET cc_start: 0.5488 (OUTLIER) cc_final: 0.4233 (mpt) REVERT: A 607 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7320 (mt0) REVERT: A 1057 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7348 (t80) REVERT: A 1204 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6278 (mpp-170) outliers start: 28 outliers final: 12 residues processed: 95 average time/residue: 0.0722 time to fit residues: 8.3666 Evaluate side-chains 73 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1365 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.164586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.139393 restraints weight = 8066.057| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.37 r_work: 0.4104 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4128 Z= 0.191 Angle : 0.717 10.792 5808 Z= 0.385 Chirality : 0.046 0.216 637 Planarity : 0.005 0.042 561 Dihedral : 27.595 177.841 962 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.27 % Allowed : 17.55 % Favored : 76.18 % 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: 0.06 (0.45), residues: 349 helix: 1.05 (0.39), residues: 174 sheet: 1.07 (1.43), residues: 12 loop : -1.18 (0.48), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 889 TYR 0.013 0.002 TYR A1300 PHE 0.025 0.002 PHE A1033 TRP 0.010 0.001 TRP A 561 HIS 0.010 0.002 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 ( 4124) covalent geometry : angle 0.66512 / 0.38 ( 5796) hydrogen bonds : bond 0.06350 / 4.26 ( 181) hydrogen bonds : angle 5.27813 / 3.73 ( 465) metal coordination : bond 0.00766 / 0.38 ( 4) metal coordination : angle 5.92404 / 3.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 607 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7473 (mt0) REVERT: A 889 ARG cc_start: 0.8257 (ttp80) cc_final: 0.8014 (tmm-80) REVERT: A 1057 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7739 (t80) REVERT: A 1204 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6434 (mpp-170) REVERT: A 1214 LEU cc_start: 0.8128 (mm) cc_final: 0.7872 (mt) outliers start: 20 outliers final: 13 residues processed: 69 average time/residue: 0.0695 time to fit residues: 5.9788 Evaluate side-chains 71 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1204 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 32 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.4564 r_free = 0.4564 target = 0.166522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.141200 restraints weight = 7830.988| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.35 r_work: 0.4124 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4128 Z= 0.145 Angle : 0.646 10.679 5808 Z= 0.345 Chirality : 0.041 0.197 637 Planarity : 0.005 0.039 561 Dihedral : 27.505 176.922 951 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.90 % Allowed : 17.24 % Favored : 75.86 % 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: 0.05 (0.45), residues: 349 helix: 1.15 (0.40), residues: 174 sheet: 0.16 (1.25), residues: 17 loop : -1.27 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 572 TYR 0.011 0.001 TYR A1300 PHE 0.017 0.002 PHE A 604 TRP 0.006 0.001 TRP A1012 HIS 0.010 0.001 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 4124) covalent geometry : angle 0.58664 / 0.35 ( 5796) hydrogen bonds : bond 0.05005 / 3.44 ( 181) hydrogen bonds : angle 4.95903 / 3.48 ( 465) metal coordination : bond 0.00586 / 0.29 ( 4) metal coordination : angle 5.96576 / 3.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 607 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7457 (mt0) REVERT: A 889 ARG cc_start: 0.8290 (ttp80) cc_final: 0.8067 (tmm-80) REVERT: A 981 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7813 (mp) REVERT: A 1057 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7705 (t80) REVERT: A 1204 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6439 (mpp-170) REVERT: A 1214 LEU cc_start: 0.8067 (mm) cc_final: 0.7812 (mt) REVERT: A 1281 THR cc_start: 0.6717 (OUTLIER) cc_final: 0.6495 (p) REVERT: A 1304 ASN cc_start: 0.8677 (p0) cc_final: 0.7797 (m110) outliers start: 22 outliers final: 15 residues processed: 72 average time/residue: 0.0648 time to fit residues: 5.8275 Evaluate side-chains 78 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.166057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.140698 restraints weight = 7874.472| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.35 r_work: 0.4116 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4128 Z= 0.144 Angle : 0.664 13.318 5808 Z= 0.342 Chirality : 0.041 0.195 637 Planarity : 0.004 0.039 561 Dihedral : 27.484 175.635 950 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.58 % Allowed : 19.12 % Favored : 74.29 % 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: 0.10 (0.45), residues: 349 helix: 1.07 (0.39), residues: 181 sheet: 0.99 (1.59), residues: 12 loop : -1.24 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 572 TYR 0.011 0.001 TYR A1300 PHE 0.018 0.002 PHE A 576 TRP 0.005 0.001 TRP A1012 HIS 0.005 0.001 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 4124) covalent geometry : angle 0.60586 / 0.34 ( 5796) hydrogen bonds : bond 0.04905 / 3.36 ( 181) hydrogen bonds : angle 4.86846 / 3.42 ( 465) metal coordination : bond 0.00521 / 0.26 ( 4) metal coordination : angle 6.03278 / 3.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.116 Fit side-chains REVERT: A 607 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7451 (mt0) REVERT: A 889 ARG cc_start: 0.8286 (ttp80) cc_final: 0.8067 (tmm-80) REVERT: A 981 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 1027 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.7328 (t-90) REVERT: A 1057 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7652 (t80) REVERT: A 1204 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6472 (mpp-170) REVERT: A 1214 LEU cc_start: 0.8110 (mm) cc_final: 0.7887 (mt) REVERT: A 1281 THR cc_start: 0.6793 (OUTLIER) cc_final: 0.6472 (p) REVERT: A 1304 ASN cc_start: 0.8633 (p0) cc_final: 0.7786 (m110) outliers start: 21 outliers final: 13 residues processed: 74 average time/residue: 0.0600 time to fit residues: 5.7149 Evaluate side-chains 76 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.166520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.141506 restraints weight = 7897.977| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.36 r_work: 0.4126 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4128 Z= 0.131 Angle : 0.646 10.584 5808 Z= 0.334 Chirality : 0.040 0.180 637 Planarity : 0.004 0.038 561 Dihedral : 27.465 175.163 945 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.96 % Allowed : 21.32 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.46), residues: 349 helix: 1.27 (0.40), residues: 179 sheet: 0.04 (1.25), residues: 21 loop : -1.31 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.009 0.001 TYR A1001 PHE 0.013 0.001 PHE A 604 TRP 0.005 0.001 TRP A1012 HIS 0.003 0.001 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 4124) covalent geometry : angle 0.58794 / 0.33 ( 5796) hydrogen bonds : bond 0.04536 / 3.13 ( 181) hydrogen bonds : angle 4.73924 / 3.31 ( 465) metal coordination : bond 0.00442 / 0.22 ( 4) metal coordination : angle 5.90707 / 3.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.084 Fit side-chains REVERT: A 607 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7434 (mt0) REVERT: A 889 ARG cc_start: 0.8302 (ttp80) cc_final: 0.8100 (tmm-80) REVERT: A 981 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7856 (mp) REVERT: A 1027 HIS cc_start: 0.7640 (OUTLIER) cc_final: 0.7120 (t-90) REVERT: A 1057 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7670 (t80) REVERT: A 1204 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6412 (mpp-170) REVERT: A 1214 LEU cc_start: 0.8076 (mm) cc_final: 0.7827 (mt) REVERT: A 1281 THR cc_start: 0.6788 (OUTLIER) cc_final: 0.6457 (p) REVERT: A 1304 ASN cc_start: 0.8578 (p0) cc_final: 0.7810 (m110) outliers start: 19 outliers final: 9 residues processed: 71 average time/residue: 0.0485 time to fit residues: 4.4506 Evaluate side-chains 71 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1204 ARG Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.165114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.138899 restraints weight = 8069.227| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.39 r_work: 0.4098 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4128 Z= 0.162 Angle : 0.674 11.232 5808 Z= 0.346 Chirality : 0.041 0.177 637 Planarity : 0.005 0.040 561 Dihedral : 27.468 174.524 941 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.27 % Allowed : 22.26 % Favored : 71.47 % 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: 0.08 (0.46), residues: 349 helix: 1.27 (0.40), residues: 179 sheet: -0.06 (1.32), residues: 19 loop : -1.46 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1204 TYR 0.012 0.002 TYR A1300 PHE 0.016 0.002 PHE A1033 TRP 0.005 0.001 TRP A 592 HIS 0.011 0.002 HIS A1203 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 4124) covalent geometry : angle 0.61088 / 0.35 ( 5796) hydrogen bonds : bond 0.04845 / 3.36 ( 181) hydrogen bonds : angle 4.73663 / 3.32 ( 465) metal coordination : bond 0.00695 / 0.35 ( 4) metal coordination : angle 6.28520 / 3.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.098 Fit side-chains REVERT: A 607 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7358 (mt0) REVERT: A 889 ARG cc_start: 0.8323 (ttp80) cc_final: 0.8117 (tmm-80) REVERT: A 981 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7950 (mp) REVERT: A 1027 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.7071 (t-90) REVERT: A 1057 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7736 (t80) REVERT: A 1214 LEU cc_start: 0.8121 (mm) cc_final: 0.7893 (mt) REVERT: A 1281 THR cc_start: 0.6798 (OUTLIER) cc_final: 0.6477 (p) REVERT: A 1304 ASN cc_start: 0.8567 (p0) cc_final: 0.7822 (m110) outliers start: 20 outliers final: 13 residues processed: 68 average time/residue: 0.0418 time to fit residues: 3.7275 Evaluate side-chains 71 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.0170 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 971 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 = 0.4558 r_free = 0.4558 target = 0.165758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.140245 restraints weight = 8086.697| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.39 r_work: 0.4111 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4128 Z= 0.138 Angle : 0.663 11.274 5808 Z= 0.338 Chirality : 0.040 0.176 637 Planarity : 0.004 0.038 561 Dihedral : 27.419 174.324 937 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.96 % Allowed : 22.57 % Favored : 71.47 % 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: 0.09 (0.46), residues: 349 helix: 1.29 (0.40), residues: 179 sheet: -0.39 (1.30), residues: 19 loop : -1.43 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1329 TYR 0.010 0.002 TYR A1300 PHE 0.013 0.002 PHE A 604 TRP 0.005 0.001 TRP A1012 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 4124) covalent geometry : angle 0.59888 / 0.34 ( 5796) hydrogen bonds : bond 0.04556 / 3.16 ( 181) hydrogen bonds : angle 4.64607 / 3.26 ( 465) metal coordination : bond 0.00484 / 0.24 ( 4) metal coordination : angle 6.28494 / 3.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.077 Fit side-chains REVERT: A 607 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7344 (mt0) REVERT: A 889 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8119 (tmm-80) REVERT: A 1027 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6995 (t-90) REVERT: A 1057 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7731 (t80) REVERT: A 1214 LEU cc_start: 0.8106 (mm) cc_final: 0.7870 (mt) REVERT: A 1281 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6488 (p) REVERT: A 1304 ASN cc_start: 0.8516 (p0) cc_final: 0.7840 (m110) outliers start: 19 outliers final: 13 residues processed: 67 average time/residue: 0.0378 time to fit residues: 3.3282 Evaluate side-chains 73 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1032 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 26 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 971 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 = 0.4578 r_free = 0.4578 target = 0.167658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.141644 restraints weight = 8209.183| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.46 r_work: 0.4126 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4128 Z= 0.126 Angle : 0.686 11.777 5808 Z= 0.331 Chirality : 0.039 0.172 637 Planarity : 0.004 0.037 561 Dihedral : 27.359 174.410 937 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.39 % Allowed : 24.45 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.46), residues: 349 helix: 1.36 (0.40), residues: 179 sheet: -0.49 (1.28), residues: 19 loop : -1.43 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1329 TYR 0.011 0.001 TYR A1001 PHE 0.011 0.001 PHE A 604 TRP 0.005 0.001 TRP A1012 HIS 0.002 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 4124) covalent geometry : angle 0.58847 / 0.33 ( 5796) hydrogen bonds : bond 0.04342 / 3.04 ( 181) hydrogen bonds : angle 4.52548 / 3.19 ( 465) metal coordination : bond 0.00322 / 0.17 ( 4) metal coordination : angle 7.77859 / 4.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 607 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7366 (mt0) REVERT: A 928 ASP cc_start: 0.7891 (p0) cc_final: 0.7494 (p0) REVERT: A 930 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: A 1057 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7680 (t80) REVERT: A 1214 LEU cc_start: 0.8100 (mm) cc_final: 0.7816 (mt) REVERT: A 1281 THR cc_start: 0.6725 (OUTLIER) cc_final: 0.6371 (p) REVERT: A 1304 ASN cc_start: 0.8455 (p0) cc_final: 0.7948 (m110) outliers start: 14 outliers final: 7 residues processed: 67 average time/residue: 0.0636 time to fit residues: 5.5224 Evaluate side-chains 66 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 971 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 = 0.4553 r_free = 0.4553 target = 0.165479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.139988 restraints weight = 8071.682| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.38 r_work: 0.4107 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4128 Z= 0.146 Angle : 0.713 11.696 5808 Z= 0.345 Chirality : 0.040 0.171 637 Planarity : 0.004 0.038 561 Dihedral : 27.373 174.070 933 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.08 % Allowed : 24.45 % Favored : 71.47 % 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: 0.10 (0.46), residues: 349 helix: 1.35 (0.41), residues: 179 sheet: -0.64 (1.26), residues: 19 loop : -1.46 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1204 TYR 0.011 0.002 TYR A1001 PHE 0.015 0.002 PHE A1033 TRP 0.005 0.001 TRP A 592 HIS 0.005 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 4124) covalent geometry : angle 0.62043 / 0.34 ( 5796) hydrogen bonds : bond 0.04600 / 3.22 ( 181) hydrogen bonds : angle 4.55559 / 3.22 ( 465) metal coordination : bond 0.00584 / 0.29 ( 4) metal coordination : angle 7.75983 / 4.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 607 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7353 (mt0) REVERT: A 980 ARG cc_start: 0.7236 (mpt180) cc_final: 0.5656 (tpt170) REVERT: A 1057 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7717 (t80) REVERT: A 1214 LEU cc_start: 0.8144 (mm) cc_final: 0.7918 (mt) REVERT: A 1281 THR cc_start: 0.6816 (OUTLIER) cc_final: 0.6493 (p) REVERT: A 1304 ASN cc_start: 0.8463 (p0) cc_final: 0.7936 (m110) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.0468 time to fit residues: 3.7617 Evaluate side-chains 63 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 971 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 = 0.4559 r_free = 0.4559 target = 0.165730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.140375 restraints weight = 8246.932| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.40 r_work: 0.4115 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4128 Z= 0.136 Angle : 0.708 11.905 5808 Z= 0.338 Chirality : 0.040 0.172 637 Planarity : 0.004 0.037 561 Dihedral : 27.329 174.010 933 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.76 % Allowed : 25.08 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.46), residues: 349 helix: 1.29 (0.40), residues: 185 sheet: -0.71 (1.23), residues: 19 loop : -1.30 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 889 TYR 0.010 0.001 TYR A1001 PHE 0.011 0.001 PHE A 604 TRP 0.004 0.001 TRP A1012 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 4124) covalent geometry : angle 0.60550 / 0.34 ( 5796) hydrogen bonds : bond 0.04353 / 3.04 ( 181) hydrogen bonds : angle 4.50461 / 3.19 ( 465) metal coordination : bond 0.00448 / 0.23 ( 4) metal coordination : angle 8.09483 / 4.36 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 607 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7347 (mt0) REVERT: A 889 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7912 (tmm-80) REVERT: A 980 ARG cc_start: 0.7209 (mpt180) cc_final: 0.5677 (tpt170) REVERT: A 1057 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7695 (t80) REVERT: A 1214 LEU cc_start: 0.8135 (mm) cc_final: 0.7907 (mt) REVERT: A 1281 THR cc_start: 0.6769 (OUTLIER) cc_final: 0.6455 (p) REVERT: A 1304 ASN cc_start: 0.8440 (p0) cc_final: 0.7953 (m110) outliers start: 12 outliers final: 8 residues processed: 61 average time/residue: 0.0479 time to fit residues: 3.8359 Evaluate side-chains 65 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 TRP Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 971 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 = 0.4554 r_free = 0.4554 target = 0.165297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.139854 restraints weight = 8210.883| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.40 r_work: 0.4106 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4128 Z= 0.140 Angle : 0.713 12.273 5808 Z= 0.340 Chirality : 0.040 0.170 637 Planarity : 0.004 0.038 561 Dihedral : 27.305 173.810 933 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.45 % Allowed : 25.39 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.46), residues: 349 helix: 1.34 (0.40), residues: 184 sheet: -0.80 (1.20), residues: 19 loop : -1.35 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 889 TYR 0.011 0.001 TYR A1300 PHE 0.014 0.001 PHE A1033 TRP 0.004 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 4124) covalent geometry : angle 0.61059 / 0.34 ( 5796) hydrogen bonds : bond 0.04508 / 3.16 ( 181) hydrogen bonds : angle 4.50725 / 3.19 ( 465) metal coordination : bond 0.00504 / 0.25 ( 4) metal coordination : angle 8.13246 / 4.40 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1145.35 seconds wall clock time: 20 minutes 18.95 seconds (1218.95 seconds total)