Starting phenix.real_space_refine on Thu Sep 10 21:36:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yho_33832/09_2026/7yho_33832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yho_33832/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7yho_33832/09_2026/7yho_33832.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yho_33832/09_2026/7yho_33832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yho_33832/09_2026/7yho_33832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yho_33832/09_2026/7yho_33832.map" model { file = "/net/cci-nas-00/data/ceres_data/7yho_33832/09_2026/7yho_33832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yho_33832/09_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-2.2.1-6174/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: 1.22, per 1000 atoms: 0.31 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: 0.43 Conformation dependent library (CDL) restraints added in 138.9 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: 0.48 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: 0.73 Time building geometry restraints manager: 0.55 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: 88 5.04 - 7.56: 10 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.000 Find NCS groups from input model: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.650 ------------------------------------------------------------------------------- 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= 0.468 Angle : 0.846 12.594 5808 Z= 0.643 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 0.80962 / 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 : 0.133 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: 0.0780 time to fit residues: 9.0790 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 : 0.134 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.164628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.139429 restraints weight = 8055.953| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.34 r_work: 0.4106 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4128 Z= 0.186 Angle : 0.726 10.821 5808 Z= 0.388 Chirality : 0.046 0.228 637 Planarity : 0.005 0.042 561 Dihedral : 27.582 177.803 962 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.58 % Allowed : 17.24 % 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: 0.02 (0.45), residues: 349 helix: 0.98 (0.39), residues: 180 sheet: 1.05 (1.44), residues: 12 loop : -1.22 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 889 TYR 0.013 0.002 TYR A1300 PHE 0.024 0.002 PHE A1033 TRP 0.011 0.001 TRP A 561 HIS 0.010 0.002 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 ( 4124) covalent geometry : angle 0.67430 / 0.39 ( 5796) hydrogen bonds : bond 0.06208 / 4.18 ( 181) hydrogen bonds : angle 5.26852 / 3.72 ( 465) metal coordination : bond 0.00740 / 0.37 ( 4) metal coordination : angle 5.95489 / 3.38 ( 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 77 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 607 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7469 (mt0) REVERT: A 889 ARG cc_start: 0.8249 (ttp80) cc_final: 0.8013 (tmm-80) REVERT: A 1057 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7723 (t80) REVERT: A 1204 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6412 (mpp-170) REVERT: A 1214 LEU cc_start: 0.8085 (mm) cc_final: 0.7831 (mt) REVERT: A 1281 THR cc_start: 0.6767 (OUTLIER) cc_final: 0.6464 (p) outliers start: 21 outliers final: 13 residues processed: 70 average time/residue: 0.0725 time to fit residues: 6.3199 Evaluate side-chains 71 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1281 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.0050 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.166529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.141191 restraints weight = 7842.882| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.34 r_work: 0.4129 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1879 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= 0.146 Angle : 0.653 10.742 5808 Z= 0.348 Chirality : 0.041 0.203 637 Planarity : 0.005 0.040 561 Dihedral : 27.485 176.840 951 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.90 % Allowed : 17.55 % Favored : 75.55 % 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 (0.45), residues: 349 helix: 1.16 (0.39), residues: 174 sheet: 0.19 (1.26), residues: 17 loop : -1.25 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 572 TYR 0.011 0.001 TYR A1300 PHE 0.016 0.002 PHE A 604 TRP 0.006 0.001 TRP A1012 HIS 0.008 0.001 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 4124) covalent geometry : angle 0.59432 / 0.35 ( 5796) hydrogen bonds : bond 0.05063 / 3.48 ( 181) hydrogen bonds : angle 4.97234 / 3.51 ( 465) metal coordination : bond 0.00531 / 0.27 ( 4) metal coordination : angle 5.97141 / 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 80 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 580 MET cc_start: 0.4951 (OUTLIER) cc_final: 0.4236 (mpt) REVERT: A 607 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7457 (mt0) REVERT: A 889 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8063 (tmm-80) REVERT: A 981 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7819 (mp) REVERT: A 1057 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7680 (t80) REVERT: A 1204 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6420 (mpp-170) REVERT: A 1214 LEU cc_start: 0.8100 (mm) cc_final: 0.7847 (mt) REVERT: A 1281 THR cc_start: 0.6719 (OUTLIER) cc_final: 0.6502 (p) REVERT: A 1304 ASN cc_start: 0.8698 (p0) cc_final: 0.7792 (m110) outliers start: 22 outliers final: 13 residues processed: 72 average time/residue: 0.0738 time to fit residues: 6.6753 Evaluate side-chains 75 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.0010 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.4554 r_free = 0.4554 target = 0.165610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.140093 restraints weight = 7899.323| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.36 r_work: 0.4112 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2113 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= 0.141 Angle : 0.667 14.458 5808 Z= 0.340 Chirality : 0.041 0.198 637 Planarity : 0.004 0.039 561 Dihedral : 27.469 175.436 948 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.27 % Allowed : 19.44 % 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: 0.16 (0.45), residues: 349 helix: 1.13 (0.40), residues: 181 sheet: 1.06 (1.61), residues: 12 loop : -1.22 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 572 TYR 0.011 0.001 TYR A1300 PHE 0.014 0.002 PHE A1033 TRP 0.005 0.001 TRP A1012 HIS 0.005 0.001 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 4124) covalent geometry : angle 0.60790 / 0.34 ( 5796) hydrogen bonds : bond 0.04870 / 3.34 ( 181) hydrogen bonds : angle 4.83958 / 3.38 ( 465) metal coordination : bond 0.00548 / 0.27 ( 4) metal coordination : angle 6.04812 / 3.45 ( 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 81 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.142 Fit side-chains REVERT: A 607 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7453 (mt0) REVERT: A 889 ARG cc_start: 0.8287 (ttp80) cc_final: 0.8077 (tmm-80) REVERT: A 981 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 1027 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7296 (t-90) REVERT: A 1057 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 1204 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6497 (mpp-170) REVERT: A 1214 LEU cc_start: 0.8100 (mm) cc_final: 0.7875 (mt) REVERT: A 1304 ASN cc_start: 0.8625 (p0) cc_final: 0.7787 (m110) outliers start: 20 outliers final: 14 residues processed: 73 average time/residue: 0.0619 time to fit residues: 5.7658 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 : 0.132 ------------------------------------------------------------------------------- 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 893 VAL 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 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 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: 1.9990 chunk 31 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.0000 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.166289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.141027 restraints weight = 7936.421| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.38 r_work: 0.4123 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2254 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= 0.132 Angle : 0.652 10.960 5808 Z= 0.336 Chirality : 0.040 0.188 637 Planarity : 0.004 0.037 561 Dihedral : 27.430 175.194 948 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.96 % Allowed : 22.26 % Favored : 71.79 % 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: 0.16 (0.46), residues: 349 helix: 1.16 (0.40), residues: 181 sheet: 0.13 (1.26), residues: 21 loop : -1.25 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 572 TYR 0.009 0.001 TYR A1300 PHE 0.020 0.002 PHE A 576 TRP 0.005 0.001 TRP A1012 HIS 0.003 0.001 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 4124) covalent geometry : angle 0.59378 / 0.34 ( 5796) hydrogen bonds : bond 0.04549 / 3.14 ( 181) hydrogen bonds : angle 4.71925 / 3.31 ( 465) metal coordination : bond 0.00442 / 0.22 ( 4) metal coordination : angle 5.94024 / 3.40 ( 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 77 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.117 Fit side-chains REVERT: A 607 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7427 (mt0) REVERT: A 981 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7916 (mp) REVERT: A 1027 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.7166 (t-90) REVERT: A 1057 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7686 (t80) REVERT: A 1204 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6381 (mpp-170) REVERT: A 1214 LEU cc_start: 0.8081 (mm) cc_final: 0.7850 (mt) REVERT: A 1281 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.6469 (p) REVERT: A 1304 ASN cc_start: 0.8558 (p0) cc_final: 0.7806 (m110) outliers start: 19 outliers final: 10 residues processed: 69 average time/residue: 0.0643 time to fit residues: 5.6884 Evaluate side-chains 72 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 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 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 963 LEU Chi-restraints excluded: chain A residue 981 LEU 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: 0.7980 chunk 31 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4554 r_free = 0.4554 target = 0.165582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.139870 restraints weight = 8105.752| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.40 r_work: 0.4111 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4128 Z= 0.150 Angle : 0.668 10.976 5808 Z= 0.342 Chirality : 0.040 0.184 637 Planarity : 0.005 0.041 561 Dihedral : 27.415 174.720 941 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.90 % Allowed : 21.32 % Favored : 71.79 % 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: 0.08 (0.46), residues: 349 helix: 1.19 (0.39), residues: 181 sheet: 0.00 (1.34), residues: 19 loop : -1.39 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1329 TYR 0.010 0.002 TYR A1300 PHE 0.014 0.002 PHE A1033 TRP 0.004 0.001 TRP A1012 HIS 0.011 0.001 HIS A1203 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 ( 4124) covalent geometry : angle 0.60782 / 0.34 ( 5796) hydrogen bonds : bond 0.04677 / 3.24 ( 181) hydrogen bonds : angle 4.69558 / 3.29 ( 465) metal coordination : bond 0.00568 / 0.28 ( 4) metal coordination : angle 6.14993 / 3.51 ( 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 78 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.130 Fit side-chains REVERT: A 607 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7389 (mt0) REVERT: A 1027 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.7126 (t-90) REVERT: A 1057 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7705 (t80) REVERT: A 1214 LEU cc_start: 0.8106 (mm) cc_final: 0.7861 (mt) REVERT: A 1281 THR cc_start: 0.6798 (OUTLIER) cc_final: 0.6481 (p) REVERT: A 1304 ASN cc_start: 0.8558 (p0) cc_final: 0.7817 (m110) outliers start: 22 outliers final: 14 residues processed: 71 average time/residue: 0.0489 time to fit residues: 4.5550 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 : 0.126 ------------------------------------------------------------------------------- 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 1031 ILE 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: 2.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.161255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.135362 restraints weight = 8110.741| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.34 r_work: 0.4048 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4128 Z= 0.214 Angle : 0.805 12.749 5808 Z= 0.389 Chirality : 0.044 0.183 637 Planarity : 0.006 0.043 561 Dihedral : 27.537 173.124 937 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.64 % Allowed : 23.82 % Favored : 70.53 % 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: -0.31 (0.46), residues: 349 helix: 0.83 (0.39), residues: 187 sheet: -0.61 (1.27), residues: 19 loop : -1.55 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1329 TYR 0.017 0.002 TYR A1300 PHE 0.025 0.003 PHE A1033 TRP 0.011 0.001 TRP A 592 HIS 0.009 0.002 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 ( 4124) covalent geometry : angle 0.69858 / 0.39 ( 5796) hydrogen bonds : bond 0.05813 / 4.01 ( 181) hydrogen bonds : angle 4.97487 / 3.52 ( 465) metal coordination : bond 0.00871 / 0.43 ( 4) metal coordination : angle 8.84805 / 4.86 ( 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 72 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.133 Fit side-chains REVERT: A 906 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7779 (m-40) REVERT: A 1027 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.7127 (t-90) REVERT: A 1057 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7875 (t80) REVERT: A 1214 LEU cc_start: 0.8192 (mm) cc_final: 0.7916 (mt) REVERT: A 1281 THR cc_start: 0.6939 (OUTLIER) cc_final: 0.6611 (p) REVERT: A 1304 ASN cc_start: 0.8595 (p0) cc_final: 0.7773 (m110) outliers start: 18 outliers final: 13 residues processed: 66 average time/residue: 0.0534 time to fit residues: 4.6883 Evaluate side-chains 68 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 1031 ILE 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: 0.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.164041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.138229 restraints weight = 8046.821| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.36 r_work: 0.4088 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2721 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= 0.151 Angle : 0.730 12.380 5808 Z= 0.353 Chirality : 0.041 0.188 637 Planarity : 0.004 0.041 561 Dihedral : 27.426 173.024 937 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.39 % Allowed : 26.33 % Favored : 69.28 % 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: 0.04 (0.47), residues: 349 helix: 1.08 (0.40), residues: 185 sheet: -0.78 (1.23), residues: 19 loop : -1.23 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1329 TYR 0.013 0.002 TYR A1300 PHE 0.014 0.002 PHE A 576 TRP 0.007 0.001 TRP A1012 HIS 0.003 0.001 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 4124) covalent geometry : angle 0.62939 / 0.35 ( 5796) hydrogen bonds : bond 0.04710 / 3.26 ( 181) hydrogen bonds : angle 4.75493 / 3.34 ( 465) metal coordination : bond 0.00437 / 0.22 ( 4) metal coordination : angle 8.14178 / 4.52 ( 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 69 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.129 Fit side-chains REVERT: A 980 ARG cc_start: 0.7115 (mpt180) cc_final: 0.5558 (tpt170) REVERT: A 1057 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7817 (t80) REVERT: A 1214 LEU cc_start: 0.8154 (mm) cc_final: 0.7899 (mt) REVERT: A 1281 THR cc_start: 0.6799 (OUTLIER) cc_final: 0.6489 (p) REVERT: A 1304 ASN cc_start: 0.8538 (p0) cc_final: 0.7805 (m110) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.0528 time to fit residues: 4.4323 Evaluate side-chains 67 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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 921 VAL 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 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: 0.6980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.162850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.137376 restraints weight = 8048.815| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.35 r_work: 0.4075 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2789 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= 0.162 Angle : 0.740 12.231 5808 Z= 0.356 Chirality : 0.041 0.184 637 Planarity : 0.005 0.042 561 Dihedral : 27.430 172.650 935 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.33 % Allowed : 25.39 % Favored : 69.28 % 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: 0.02 (0.47), residues: 349 helix: 1.06 (0.40), residues: 185 sheet: -0.79 (1.22), residues: 19 loop : -1.25 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1329 TYR 0.014 0.002 TYR A1300 PHE 0.017 0.002 PHE A1033 TRP 0.004 0.001 TRP A 592 HIS 0.005 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 4124) covalent geometry : angle 0.63917 / 0.36 ( 5796) hydrogen bonds : bond 0.04876 / 3.40 ( 181) hydrogen bonds : angle 4.74263 / 3.34 ( 465) metal coordination : bond 0.00568 / 0.28 ( 4) metal coordination : angle 8.23510 / 4.57 ( 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 72 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.138 Fit side-chains REVERT: A 980 ARG cc_start: 0.7165 (mpt180) cc_final: 0.5636 (tpt170) REVERT: A 1057 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7845 (t80) REVERT: A 1214 LEU cc_start: 0.8168 (mm) cc_final: 0.7919 (mt) REVERT: A 1281 THR cc_start: 0.6831 (OUTLIER) cc_final: 0.6509 (p) REVERT: A 1304 ASN cc_start: 0.8544 (p0) cc_final: 0.7819 (m110) outliers start: 17 outliers final: 12 residues processed: 66 average time/residue: 0.0509 time to fit residues: 4.4742 Evaluate side-chains 70 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 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 882 THR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 921 VAL 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 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: 0.0870 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.4566 r_free = 0.4566 target = 0.165940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.140199 restraints weight = 8005.608| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.38 r_work: 0.4111 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2920 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= 0.134 Angle : 0.737 12.055 5808 Z= 0.352 Chirality : 0.040 0.182 637 Planarity : 0.004 0.040 561 Dihedral : 27.342 173.212 935 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.76 % Allowed : 26.02 % Favored : 70.22 % 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: 0.01 (0.46), residues: 349 helix: 1.05 (0.40), residues: 185 sheet: -0.80 (1.21), residues: 19 loop : -1.24 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1329 TYR 0.010 0.001 TYR A1001 PHE 0.011 0.001 PHE A 576 TRP 0.007 0.001 TRP A1012 HIS 0.002 0.001 HIS A1027 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 4124) covalent geometry : angle 0.63840 / 0.35 ( 5796) hydrogen bonds : bond 0.04432 / 3.09 ( 181) hydrogen bonds : angle 4.58959 / 3.24 ( 465) metal coordination : bond 0.00423 / 0.22 ( 4) metal coordination : angle 8.12418 / 4.43 ( 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 70 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.112 Fit side-chains REVERT: A 980 ARG cc_start: 0.7138 (mpt180) cc_final: 0.5611 (tpt170) REVERT: A 1057 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7791 (t80) REVERT: A 1214 LEU cc_start: 0.8116 (mm) cc_final: 0.7856 (mt) REVERT: A 1281 THR cc_start: 0.6714 (OUTLIER) cc_final: 0.6394 (p) REVERT: A 1304 ASN cc_start: 0.8437 (p0) cc_final: 0.7915 (m110) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.0544 time to fit residues: 4.6347 Evaluate side-chains 66 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 906 ASN Chi-restraints excluded: chain A residue 921 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 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: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.162230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.136474 restraints weight = 8036.159| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.35 r_work: 0.4060 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4128 Z= 0.194 Angle : 0.793 12.716 5808 Z= 0.380 Chirality : 0.042 0.180 637 Planarity : 0.005 0.041 561 Dihedral : 27.384 172.352 933 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.70 % Allowed : 25.39 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.46), residues: 349 helix: 1.03 (0.40), residues: 185 sheet: -0.88 (1.21), residues: 19 loop : -1.41 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1329 TYR 0.015 0.002 TYR A1300 PHE 0.021 0.002 PHE A1033 TRP 0.007 0.001 TRP A 592 HIS 0.007 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 4124) covalent geometry : angle 0.69316 / 0.38 ( 5796) hydrogen bonds : bond 0.05168 / 3.62 ( 181) hydrogen bonds : angle 4.68778 / 3.31 ( 465) metal coordination : bond 0.00788 / 0.39 ( 4) metal coordination : angle 8.51589 / 4.69 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1278.56 seconds wall clock time: 22 minutes 54.84 seconds (1374.84 seconds total)