Starting phenix.real_space_refine on Thu Sep 10 21:48:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yhq_33836/09_2026/7yhq_33836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yhq_33836/09_2026/7yhq_33836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yhq_33836/09_2026/7yhq_33836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yhq_33836/09_2026/7yhq_33836.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yhq_33836/09_2026/7yhq_33836.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yhq_33836/09_2026/7yhq_33836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yhq_33836/09_2026/7yhq_33836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yhq_33836/09_2026/7yhq_33836.map" } resolution = 3.9 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 43 5.49 5 S 23 5.16 5 C 2461 2.51 5 N 726 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4065 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3182 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 25, 'TRANS': 367} Chain breaks: 4 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: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 181 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 155 Unusual residues: {'PED': 1} Classifications: {'DNA': 7, 'undetermined': 1} Link IDs: {'rna3p': 6, None: 1} Not linked: pdbres="PED C 26 " pdbres=" DG C 27 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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 1949 SG CYS A1045 55.589 28.918 53.222 1.00 76.27 S ATOM 1897 SG CYS A1038 52.380 29.895 47.604 1.00 69.77 S ATOM 1968 SG CYS A1048 52.542 24.215 49.877 1.00 71.00 S ATOM 2011 SG CYS A1054 57.449 28.416 49.055 1.00 77.53 S Time building chain proxies: 1.05, per 1000 atoms: 0.26 Number of scatterers: 4065 At special positions: 0 Unit cell: (86.43, 72.36, 86.43, 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 43 15.00 O 808 8.00 N 726 7.00 C 2461 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 138.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A1038 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A1048 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A1054 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A1045 " Number of angles added : 12 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 55.7% alpha, 3.8% beta 13 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 560 through 580 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 595 through 606 removed outlier: 3.960A pdb=" N SER A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 625 Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.626A pdb=" N ILE A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 905 through 925 Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 936 through 946 Processing helix chain 'A' and resid 951 through 964 removed outlier: 4.180A pdb=" N VAL A 955 " --> pdb=" O GLY A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 981 Processing helix chain 'A' and resid 1007 through 1012 Processing helix chain 'A' and resid 1013 through 1016 removed outlier: 3.977A pdb=" N CYS A1016 " --> pdb=" O PRO A1013 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1013 through 1016' Processing helix chain 'A' and resid 1019 through 1037 Processing helix chain 'A' and resid 1044 through 1053 Proline residue: A1049 - end of helix removed outlier: 4.182A pdb=" N GLY A1052 " --> pdb=" O PRO A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1059 removed outlier: 3.536A pdb=" N ALA A1058 " --> pdb=" O CYS A1054 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A1059 " --> pdb=" O ARG A1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1054 through 1059' Processing helix chain 'A' and resid 1212 through 1216 Processing helix chain 'A' and resid 1286 through 1291 Processing helix chain 'A' and resid 1294 through 1299 removed outlier: 3.509A pdb=" N ASN A1297 " --> pdb=" O PHE A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1315 Processing helix chain 'A' and resid 1337 through 1343 removed outlier: 3.614A pdb=" N ILE A1341 " --> pdb=" O SER A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1356 Processing sheet with id=AA1, first strand: chain 'A' and resid 1306 through 1308 removed outlier: 3.956A pdb=" N TYR A1229 " --> pdb=" O LEU A1208 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A1206 " --> pdb=" O LEU A1231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1363 through 1364 removed outlier: 3.723A pdb=" N GLY A1363 " --> pdb=" O LYS A1372 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A1372 " --> pdb=" O GLY A1363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 135 hydrogen bonds defined for protein. 369 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 1865 1.43 - 1.64: 2351 1.64 - 1.85: 28 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 4256 Sorted by residual: bond pdb=" O1P PED C 26 " pdb=" P PED C 26 " ideal model delta sigma weight residual 1.679 1.469 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CA ASN A1044 " pdb=" C ASN A1044 " ideal model delta sigma weight residual 1.531 1.474 0.057 1.12e-02 7.97e+03 2.57e+01 bond pdb=" N9 DA B 7 " pdb=" C4 DA B 7 " ideal model delta sigma weight residual 1.374 1.396 -0.022 6.00e-03 2.78e+04 1.31e+01 bond pdb=" C3' DC B 4 " pdb=" C2' DC B 4 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.21e+00 bond pdb=" N THR A 962 " pdb=" CA THR A 962 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.17e-02 7.31e+03 7.22e+00 ... (remaining 4251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 5715 2.20 - 4.39: 196 4.39 - 6.59: 26 6.59 - 8.78: 6 8.78 - 10.98: 4 Bond angle restraints: 5947 Sorted by residual: angle pdb=" N ASN A1044 " pdb=" CA ASN A1044 " pdb=" C ASN A1044 " ideal model delta sigma weight residual 110.70 100.96 9.74 1.55e+00 4.16e-01 3.95e+01 angle pdb=" C PHE A 625 " pdb=" N PRO A 626 " pdb=" CA PRO A 626 " ideal model delta sigma weight residual 120.14 113.74 6.40 1.06e+00 8.90e-01 3.65e+01 angle pdb=" C3' DT B 5 " pdb=" O3' DT B 5 " pdb=" P DG B 6 " ideal model delta sigma weight residual 119.70 113.50 6.20 1.20e+00 6.94e-01 2.67e+01 angle pdb=" N TRP A 561 " pdb=" CA TRP A 561 " pdb=" C TRP A 561 " ideal model delta sigma weight residual 111.82 106.16 5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" N ASN A1046 " pdb=" CA ASN A1046 " pdb=" C ASN A1046 " ideal model delta sigma weight residual 111.82 106.35 5.47 1.16e+00 7.43e-01 2.22e+01 ... (remaining 5942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 2176 35.85 - 71.69: 239 71.69 - 107.53: 10 107.53 - 143.38: 0 143.38 - 179.22: 2 Dihedral angle restraints: 2427 sinusoidal: 1285 harmonic: 1142 Sorted by residual: dihedral pdb=" CA TYR A1001 " pdb=" C TYR A1001 " pdb=" N PRO A1002 " pdb=" CA PRO A1002 " ideal model delta harmonic sigma weight residual -180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+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 -140.00 39.22 -179.22 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT B 12 " pdb=" C3' DT B 12 " pdb=" O3' DT B 12 " pdb=" P DC B 13 " ideal model delta sinusoidal sigma weight residual 220.00 51.30 168.70 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 2424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 625 0.104 - 0.207: 23 0.207 - 0.311: 4 0.311 - 0.415: 1 0.415 - 0.518: 3 Chirality restraints: 656 Sorted by residual: 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 -2.85 -0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" P DT B 5 " pdb=" OP1 DT B 5 " pdb=" OP2 DT B 5 " pdb=" O5' DT B 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.49 2.00e-01 2.50e+01 6.01e+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 5.86e+00 ... (remaining 653 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 561 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C TRP A 561 " 0.034 2.00e-02 2.50e+03 pdb=" O TRP A 561 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP A 562 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 27 " 0.018 2.00e-02 2.50e+03 1.02e-02 3.11e+00 pdb=" N9 DG C 27 " -0.008 2.00e-02 2.50e+03 pdb=" C8 DG C 27 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG C 27 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG C 27 " -0.020 2.00e-02 2.50e+03 pdb=" C6 DG C 27 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG C 27 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DG C 27 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DG C 27 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG C 27 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG C 27 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG C 27 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 627 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 628 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " 0.024 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 851 2.78 - 3.31: 3854 3.31 - 3.84: 7214 3.84 - 4.37: 8241 4.37 - 4.90: 12622 Nonbonded interactions: 32782 Sorted by model distance: nonbonded pdb=" O TYR A 943 " pdb=" OG SER A 946 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A1024 " pdb=" OD1 ASN A1297 " model vdw 2.280 3.040 nonbonded pdb=" O MET A1050 " pdb=" N CYS A1054 " model vdw 2.287 3.120 nonbonded pdb=" OG SER A 623 " pdb=" O THR A1368 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLN A 987 " pdb=" N SER A 992 " model vdw 2.341 3.120 ... (remaining 32777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 6.260 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: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.210 4263 Z= 0.443 Angle : 1.464 54.076 5959 Z= 0.600 Chirality : 0.063 0.518 656 Planarity : 0.005 0.041 604 Dihedral : 24.124 179.224 1683 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.00 % Allowed : 1.71 % Favored : 96.29 % 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: -0.58 (0.46), residues: 383 helix: 1.04 (0.43), residues: 170 sheet: -2.96 (0.87), residues: 20 loop : -1.43 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1221 TYR 0.022 0.002 TYR A1001 PHE 0.012 0.002 PHE A1354 TRP 0.014 0.001 TRP A1355 HIS 0.003 0.001 HIS A1212 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.40 ( 4256) covalent geometry : angle 0.93635 / 0.59 ( 5947) hydrogen bonds : bond 0.20386 / 13.97 ( 167) hydrogen bonds : angle 9.05802 / 6.32 ( 433) metal coordination : bond 0.05504 / 2.67 ( 4) metal coordination : angle 25.08588 / 13.67 ( 12) Misc. bond : bond 0.06755 / 3.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.144 Fit side-chains REVERT: A 566 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6823 (mtt-85) REVERT: A 901 LYS cc_start: 0.8605 (ptmt) cc_final: 0.8328 (ptpt) REVERT: A 929 LEU cc_start: 0.8896 (mt) cc_final: 0.8632 (mp) REVERT: A 1378 LEU cc_start: 0.7059 (mt) cc_final: 0.6671 (mp) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.0889 time to fit residues: 7.7506 Evaluate side-chains 50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 1038 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 973 ASN A1008 GLN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.130062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106093 restraints weight = 11992.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108557 restraints weight = 7028.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.110278 restraints weight = 4932.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.111290 restraints weight = 3927.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.112232 restraints weight = 3407.674| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4263 Z= 0.165 Angle : 1.250 44.756 5959 Z= 0.399 Chirality : 0.047 0.316 656 Planarity : 0.006 0.045 604 Dihedral : 27.864 177.197 907 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.43 % Allowed : 11.14 % Favored : 87.43 % 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: -0.77 (0.46), residues: 383 helix: 0.94 (0.42), residues: 173 sheet: -3.32 (0.81), residues: 22 loop : -1.58 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1330 TYR 0.015 0.002 TYR A1001 PHE 0.021 0.002 PHE A 569 TRP 0.025 0.002 TRP A 562 HIS 0.003 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 4256) covalent geometry : angle 0.72913 / 0.39 ( 5947) hydrogen bonds : bond 0.06467 / 4.23 ( 167) hydrogen bonds : angle 5.77603 / 4.05 ( 433) metal coordination : bond 0.01560 / 0.76 ( 4) metal coordination : angle 22.64698 / 12.75 ( 12) Misc. bond : bond 0.00490 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.127 Fit side-chains REVERT: A 619 MET cc_start: 0.8658 (mtp) cc_final: 0.8406 (mtm) REVERT: A 929 LEU cc_start: 0.9156 (mt) cc_final: 0.8870 (mp) REVERT: A 942 GLU cc_start: 0.8231 (tm-30) cc_final: 0.8007 (tt0) REVERT: A 1378 LEU cc_start: 0.7203 (mt) cc_final: 0.6808 (mp) outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.0618 time to fit residues: 4.5894 Evaluate side-chains 47 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1038 CYS Chi-restraints excluded: chain A residue 1039 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 567 ASN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.129502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.105255 restraints weight = 11874.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.107713 restraints weight = 7146.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.109290 restraints weight = 5074.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.110591 restraints weight = 4088.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.111247 restraints weight = 3531.966| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4263 Z= 0.153 Angle : 1.155 41.894 5959 Z= 0.374 Chirality : 0.045 0.315 656 Planarity : 0.005 0.038 604 Dihedral : 27.686 179.504 903 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.86 % Allowed : 14.29 % Favored : 82.86 % 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: -0.87 (0.45), residues: 383 helix: 0.96 (0.41), residues: 171 sheet: -3.69 (0.75), residues: 22 loop : -1.68 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1221 TYR 0.011 0.002 TYR A1001 PHE 0.010 0.001 PHE A 576 TRP 0.010 0.002 TRP A 561 HIS 0.002 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 4256) covalent geometry : angle 0.67612 / 0.37 ( 5947) hydrogen bonds : bond 0.05971 / 3.89 ( 167) hydrogen bonds : angle 5.62059 / 3.93 ( 433) metal coordination : bond 0.01164 / 0.59 ( 4) metal coordination : angle 20.87147 / 11.84 ( 12) Misc. bond : bond 0.00120 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 619 MET cc_start: 0.8663 (mtp) cc_final: 0.8443 (mtm) REVERT: A 929 LEU cc_start: 0.9177 (mt) cc_final: 0.8867 (mp) REVERT: A 1003 MET cc_start: 0.6568 (tpp) cc_final: 0.6180 (tpp) REVERT: A 1378 LEU cc_start: 0.7218 (mt) cc_final: 0.6802 (mp) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.0621 time to fit residues: 4.5576 Evaluate side-chains 47 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1038 CYS Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1319 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** 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 = 0.4113 r_free = 0.4113 target = 0.129339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.105029 restraints weight = 11985.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107509 restraints weight = 7204.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.109264 restraints weight = 5172.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.110451 restraints weight = 4118.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.111132 restraints weight = 3546.777| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4263 Z= 0.141 Angle : 1.069 39.039 5959 Z= 0.357 Chirality : 0.043 0.305 656 Planarity : 0.005 0.035 604 Dihedral : 27.511 178.534 899 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.86 % Allowed : 13.71 % Favored : 83.43 % 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: -0.88 (0.45), residues: 383 helix: 1.02 (0.42), residues: 172 sheet: -3.69 (0.76), residues: 22 loop : -1.77 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 570 TYR 0.011 0.002 TYR A1001 PHE 0.009 0.001 PHE A1033 TRP 0.013 0.001 TRP A 562 HIS 0.002 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 4256) covalent geometry : angle 0.63783 / 0.35 ( 5947) hydrogen bonds : bond 0.05153 / 3.40 ( 167) hydrogen bonds : angle 5.37457 / 3.76 ( 433) metal coordination : bond 0.01075 / 0.54 ( 4) metal coordination : angle 19.12949 / 10.93 ( 12) Misc. bond : bond 0.00064 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 929 LEU cc_start: 0.9193 (mt) cc_final: 0.8879 (mp) REVERT: A 942 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 1003 MET cc_start: 0.6450 (tpp) cc_final: 0.6132 (tpp) REVERT: A 1378 LEU cc_start: 0.7187 (mt) cc_final: 0.6774 (mp) outliers start: 10 outliers final: 9 residues processed: 51 average time/residue: 0.0396 time to fit residues: 2.9641 Evaluate side-chains 48 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1038 CYS Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1319 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 HIS ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.124858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101352 restraints weight = 12052.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103409 restraints weight = 7559.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104934 restraints weight = 5560.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105901 restraints weight = 4515.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106615 restraints weight = 3952.329| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 4263 Z= 0.211 Angle : 1.125 40.849 5959 Z= 0.398 Chirality : 0.047 0.302 656 Planarity : 0.006 0.044 604 Dihedral : 27.519 178.344 899 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 4.00 % Allowed : 16.57 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.45), residues: 383 helix: 0.77 (0.41), residues: 172 sheet: -3.65 (0.79), residues: 22 loop : -2.03 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 566 TYR 0.017 0.002 TYR A1028 PHE 0.010 0.002 PHE A1307 TRP 0.020 0.002 TRP A 562 HIS 0.004 0.001 HIS A 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 ( 4256) covalent geometry : angle 0.72672 / 0.39 ( 5947) hydrogen bonds : bond 0.06349 / 4.04 ( 167) hydrogen bonds : angle 5.73522 / 4.03 ( 433) metal coordination : bond 0.01890 / 0.97 ( 4) metal coordination : angle 19.14975 / 11.08 ( 12) Misc. bond : bond 0.00172 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 905 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7080 (mtm) outliers start: 14 outliers final: 10 residues processed: 53 average time/residue: 0.0405 time to fit residues: 3.0900 Evaluate side-chains 51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1038 CYS Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1338 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** 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 = 0.4072 r_free = 0.4072 target = 0.125839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.102052 restraints weight = 12107.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.104459 restraints weight = 7174.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.106176 restraints weight = 5085.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107114 restraints weight = 4037.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.107923 restraints weight = 3487.447| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4263 Z= 0.163 Angle : 1.085 39.598 5959 Z= 0.379 Chirality : 0.046 0.296 656 Planarity : 0.005 0.034 604 Dihedral : 27.475 176.537 899 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.43 % Allowed : 19.14 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.45), residues: 383 helix: 0.79 (0.41), residues: 172 sheet: -3.69 (0.81), residues: 22 loop : -1.96 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 566 TYR 0.012 0.002 TYR A1028 PHE 0.010 0.001 PHE A1033 TRP 0.028 0.001 TRP A 562 HIS 0.006 0.001 HIS A1203 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 4256) covalent geometry : angle 0.70712 / 0.37 ( 5947) hydrogen bonds : bond 0.05229 / 3.42 ( 167) hydrogen bonds : angle 5.42780 / 3.82 ( 433) metal coordination : bond 0.01400 / 0.71 ( 4) metal coordination : angle 18.36342 / 10.70 ( 12) Misc. bond : bond 0.00087 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 905 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7231 (mtm) REVERT: A 942 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8019 (tt0) outliers start: 12 outliers final: 10 residues processed: 47 average time/residue: 0.0485 time to fit residues: 3.2613 Evaluate side-chains 50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1038 CYS Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1319 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** 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 = 0.4092 r_free = 0.4092 target = 0.127113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103782 restraints weight = 12112.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106090 restraints weight = 7394.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107606 restraints weight = 5300.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.108715 restraints weight = 4272.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.109323 restraints weight = 3687.003| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.003 0.034 4263 Z= 0.139 Angle : 1.024 36.174 5959 Z= 0.361 Chirality : 0.044 0.284 656 Planarity : 0.004 0.033 604 Dihedral : 27.403 175.985 899 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 3.71 % Allowed : 19.14 % Favored : 77.14 % 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: -0.99 (0.45), residues: 383 helix: 1.01 (0.42), residues: 172 sheet: -3.85 (0.72), residues: 26 loop : -1.83 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.011 0.001 TYR A1028 PHE 0.011 0.001 PHE A1033 TRP 0.028 0.001 TRP A 562 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 4256) covalent geometry : angle 0.67440 / 0.36 ( 5947) hydrogen bonds : bond 0.04822 / 3.17 ( 167) hydrogen bonds : angle 5.36321 / 3.82 ( 433) metal coordination : bond 0.00856 / 0.43 ( 4) metal coordination : angle 17.19410 / 10.03 ( 12) Misc. bond : bond 0.00089 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 905 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7099 (mtt) REVERT: A 942 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7745 (tm-30) outliers start: 13 outliers final: 8 residues processed: 53 average time/residue: 0.0474 time to fit residues: 3.5999 Evaluate side-chains 50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1038 CYS Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1045 CYS Chi-restraints excluded: chain A residue 1319 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 36 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** 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 = 0.4092 r_free = 0.4092 target = 0.127287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.105470 restraints weight = 12023.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107781 restraints weight = 7120.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.109457 restraints weight = 4979.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.110618 restraints weight = 3938.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.111204 restraints weight = 3358.665| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4263 Z= 0.136 Angle : 1.001 34.656 5959 Z= 0.363 Chirality : 0.045 0.284 656 Planarity : 0.005 0.035 604 Dihedral : 27.371 175.277 899 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.43 % Allowed : 20.29 % Favored : 76.29 % 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: -0.94 (0.45), residues: 383 helix: 1.03 (0.41), residues: 172 sheet: -3.71 (0.81), residues: 22 loop : -1.87 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1221 TYR 0.008 0.001 TYR A1028 PHE 0.017 0.001 PHE A 618 TRP 0.028 0.001 TRP A 562 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 4256) covalent geometry : angle 0.68212 / 0.36 ( 5947) hydrogen bonds : bond 0.04689 / 3.05 ( 167) hydrogen bonds : angle 5.18577 / 3.68 ( 433) metal coordination : bond 0.00778 / 0.39 ( 4) metal coordination : angle 16.33293 / 9.52 ( 12) Misc. bond : bond 0.00061 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 1351 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8213 (tp40) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.0458 time to fit residues: 3.5854 Evaluate side-chains 51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1038 CYS Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1045 CYS Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1351 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.2980 chunk 38 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 607 GLN ** 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 = 0.4108 r_free = 0.4108 target = 0.128306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106442 restraints weight = 12513.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.108917 restraints weight = 7253.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.110507 restraints weight = 5046.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.111785 restraints weight = 3982.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.112427 restraints weight = 3373.948| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4263 Z= 0.134 Angle : 0.995 34.019 5959 Z= 0.367 Chirality : 0.044 0.291 656 Planarity : 0.005 0.038 604 Dihedral : 27.351 174.835 899 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.00 % Allowed : 22.29 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.45), residues: 383 helix: 0.88 (0.41), residues: 173 sheet: -3.94 (0.70), residues: 26 loop : -1.78 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1287 TYR 0.008 0.001 TYR A1028 PHE 0.015 0.001 PHE A 618 TRP 0.029 0.002 TRP A 562 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 4256) covalent geometry : angle 0.69268 / 0.36 ( 5947) hydrogen bonds : bond 0.04557 / 3.02 ( 167) hydrogen bonds : angle 5.29219 / 3.77 ( 433) metal coordination : bond 0.00654 / 0.33 ( 4) metal coordination : angle 15.92499 / 9.28 ( 12) Misc. bond : bond 0.00056 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 942 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7895 (tm-30) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.0473 time to fit residues: 3.4953 Evaluate side-chains 48 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 1038 CYS Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1045 CYS Chi-restraints excluded: chain A residue 1319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** 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 = 0.4102 r_free = 0.4102 target = 0.127878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.104533 restraints weight = 12126.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107062 restraints weight = 7223.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.108806 restraints weight = 5115.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.109911 restraints weight = 4075.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.110499 restraints weight = 3510.628| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4263 Z= 0.138 Angle : 0.993 33.579 5959 Z= 0.367 Chirality : 0.045 0.293 656 Planarity : 0.005 0.041 604 Dihedral : 27.346 174.590 898 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.00 % Allowed : 22.57 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.45), residues: 383 helix: 0.86 (0.41), residues: 173 sheet: -3.80 (0.71), residues: 26 loop : -1.79 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.008 0.001 TYR A1028 PHE 0.016 0.001 PHE A 618 TRP 0.029 0.001 TRP A 562 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 4256) covalent geometry : angle 0.69880 / 0.36 ( 5947) hydrogen bonds : bond 0.04514 / 2.96 ( 167) hydrogen bonds : angle 5.22752 / 3.71 ( 433) metal coordination : bond 0.00680 / 0.34 ( 4) metal coordination : angle 15.72963 / 9.19 ( 12) Misc. bond : bond 0.00054 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 942 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7942 (tm-30) outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 0.0400 time to fit residues: 2.9541 Evaluate side-chains 50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1038 CYS Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1045 CYS Chi-restraints excluded: chain A residue 1319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 607 GLN ** 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 = 0.4057 r_free = 0.4057 target = 0.124258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.101544 restraints weight = 12231.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.103614 restraints weight = 7606.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.105108 restraints weight = 5557.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.106110 restraints weight = 4540.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.106536 restraints weight = 3965.822| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4263 Z= 0.180 Angle : 1.080 37.141 5959 Z= 0.397 Chirality : 0.047 0.305 656 Planarity : 0.005 0.035 604 Dihedral : 27.428 174.581 898 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 2.00 % Allowed : 23.43 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.45), residues: 383 helix: 0.63 (0.40), residues: 178 sheet: -3.71 (0.73), residues: 26 loop : -1.72 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 566 TYR 0.015 0.002 TYR A1028 PHE 0.019 0.002 PHE A 576 TRP 0.025 0.002 TRP A 562 HIS 0.004 0.001 HIS A1203 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 4256) covalent geometry : angle 0.76287 / 0.39 ( 5947) hydrogen bonds : bond 0.05431 / 3.46 ( 167) hydrogen bonds : angle 5.52232 / 3.93 ( 433) metal coordination : bond 0.01211 / 0.61 ( 4) metal coordination : angle 17.06189 / 10.01 ( 12) Misc. bond : bond 0.00074 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 902.36 seconds wall clock time: 16 minutes 21.85 seconds (981.85 seconds total)