Starting phenix.real_space_refine on Wed Jul 1 23:29:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yhq_33836/07_2026/7yhq_33836.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yhq_33836/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yhq_33836/07_2026/7yhq_33836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yhq_33836/07_2026/7yhq_33836.map" model { file = "/net/cci-nas-00/data/ceres_data/7yhq_33836/07_2026/7yhq_33836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yhq_33836/07_2026/7yhq_33836.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yhq_33836/07_2026/7yhq_33836.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yhq_33836/07_2026/7yhq_33836.cif" } 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-dev-6108/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: 0.95, per 1000 atoms: 0.23 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: 0.39 Conformation dependent library (CDL) restraints added in 110.7 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: 0.47 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: 0.57 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 5718 2.20 - 4.39: 193 4.39 - 6.59: 25 6.59 - 8.78: 7 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=" 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 angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.16e+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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 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: 0.020 Set scattering table: 0.010 Process input model: 5.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.490 ------------------------------------------------------------------------------- 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= 0.441 Angle : 1.463 54.076 5959 Z= 0.596 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 0.93484 / 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 : 0.142 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: 0.0794 time to fit residues: 6.9603 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 : 0.129 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.129858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106182 restraints weight = 11970.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.108702 restraints weight = 7198.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.110393 restraints weight = 5110.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.111570 restraints weight = 4073.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.112297 restraints weight = 3496.265| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4263 Z= 0.164 Angle : 1.245 45.254 5959 Z= 0.393 Chirality : 0.047 0.300 656 Planarity : 0.006 0.044 604 Dihedral : 27.915 177.812 907 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.71 % Allowed : 10.00 % Favored : 88.29 % 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: -0.75 (0.46), residues: 383 helix: 0.96 (0.42), residues: 173 sheet: -3.29 (0.81), residues: 22 loop : -1.56 (0.50), 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 0.001 TRP A 562 HIS 0.003 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 4256) covalent geometry : angle 0.71691 / 0.38 ( 5947) hydrogen bonds : bond 0.06687 / 4.40 ( 167) hydrogen bonds : angle 5.81847 / 4.08 ( 433) metal coordination : bond 0.01402 / 0.69 ( 4) metal coordination : angle 22.69289 / 12.74 ( 12) Misc. bond : bond 0.00554 / 0.29 ( 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 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 619 MET cc_start: 0.8527 (mtp) cc_final: 0.8309 (mtm) REVERT: A 929 LEU cc_start: 0.9070 (mt) cc_final: 0.8769 (mp) REVERT: A 1378 LEU cc_start: 0.7142 (mt) cc_final: 0.6743 (mp) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.0528 time to fit residues: 3.9083 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 : 0.079 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 chunk 9 optimal weight: 0.3980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.131009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.106628 restraints weight = 11802.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.109159 restraints weight = 7074.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.110950 restraints weight = 5019.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.111964 restraints weight = 3996.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.112864 restraints weight = 3471.542| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4263 Z= 0.142 Angle : 1.123 41.319 5959 Z= 0.366 Chirality : 0.044 0.299 656 Planarity : 0.005 0.039 604 Dihedral : 27.653 178.596 907 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.57 % Allowed : 14.57 % 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: -0.78 (0.45), residues: 383 helix: 1.08 (0.41), residues: 171 sheet: -3.68 (0.75), residues: 22 loop : -1.67 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1221 TYR 0.011 0.001 TYR A1001 PHE 0.010 0.001 PHE A 576 TRP 0.010 0.001 TRP A 562 HIS 0.002 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 4256) covalent geometry : angle 0.65861 / 0.36 ( 5947) hydrogen bonds : bond 0.05682 / 3.72 ( 167) hydrogen bonds : angle 5.57070 / 3.89 ( 433) metal coordination : bond 0.00801 / 0.40 ( 4) metal coordination : angle 20.29155 / 11.48 ( 12) Misc. bond : bond 0.00264 / 0.13 ( 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 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.135 Fit side-chains REVERT: A 929 LEU cc_start: 0.9156 (mt) cc_final: 0.8849 (mp) REVERT: A 1003 MET cc_start: 0.6522 (tpp) cc_final: 0.6084 (tpp) REVERT: A 1378 LEU cc_start: 0.7191 (mt) cc_final: 0.6776 (mp) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.0606 time to fit residues: 4.3660 Evaluate side-chains 46 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 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: 0.8980 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.0870 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.130830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.106471 restraints weight = 11949.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.108942 restraints weight = 7149.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.110751 restraints weight = 5102.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.111656 restraints weight = 4074.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.112600 restraints weight = 3563.654| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4263 Z= 0.136 Angle : 1.048 39.027 5959 Z= 0.352 Chirality : 0.043 0.286 656 Planarity : 0.005 0.041 604 Dihedral : 27.530 178.100 899 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.57 % Allowed : 14.29 % Favored : 83.14 % 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: -0.86 (0.45), residues: 383 helix: 0.98 (0.41), residues: 172 sheet: -3.66 (0.76), residues: 22 loop : -1.70 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 566 TYR 0.010 0.001 TYR A1001 PHE 0.010 0.001 PHE A1033 TRP 0.009 0.001 TRP A 562 HIS 0.001 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 ( 4256) covalent geometry : angle 0.62828 / 0.35 ( 5947) hydrogen bonds : bond 0.05217 / 3.41 ( 167) hydrogen bonds : angle 5.35280 / 3.75 ( 433) metal coordination : bond 0.01080 / 0.54 ( 4) metal coordination : angle 18.69669 / 10.62 ( 12) Misc. bond : bond 0.00124 / 0.06 ( 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 56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 562 TRP cc_start: 0.6400 (t-100) cc_final: 0.5712 (t60) REVERT: A 929 LEU cc_start: 0.9169 (mt) cc_final: 0.8877 (mp) REVERT: A 942 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 1003 MET cc_start: 0.6582 (tpp) cc_final: 0.6220 (tpp) REVERT: A 1378 LEU cc_start: 0.7176 (mt) cc_final: 0.6770 (mp) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.0447 time to fit residues: 3.3430 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 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: 0.9980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.127747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.105185 restraints weight = 12077.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.107604 restraints weight = 7110.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.109017 restraints weight = 4982.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.110357 restraints weight = 4010.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.110888 restraints weight = 3415.993| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4263 Z= 0.161 Angle : 1.041 38.667 5959 Z= 0.361 Chirality : 0.044 0.281 656 Planarity : 0.005 0.046 604 Dihedral : 27.443 177.349 899 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 3.71 % Allowed : 16.57 % Favored : 79.71 % 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: -0.88 (0.45), residues: 383 helix: 1.06 (0.41), residues: 172 sheet: -3.67 (0.77), residues: 22 loop : -1.81 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1221 TYR 0.015 0.002 TYR A1028 PHE 0.009 0.002 PHE A1334 TRP 0.013 0.001 TRP A 562 HIS 0.003 0.001 HIS A 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 4256) covalent geometry : angle 0.66058 / 0.35 ( 5947) hydrogen bonds : bond 0.05427 / 3.56 ( 167) hydrogen bonds : angle 5.46403 / 3.86 ( 433) metal coordination : bond 0.01232 / 0.62 ( 4) metal coordination : angle 17.94084 / 10.31 ( 12) Misc. bond : bond 0.00039 / 0.02 ( 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 51 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 562 TRP cc_start: 0.6404 (t-100) cc_final: 0.5591 (t60) REVERT: A 619 MET cc_start: 0.8756 (mtp) cc_final: 0.8542 (mtm) REVERT: A 905 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7205 (mtm) REVERT: A 942 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8005 (tm-30) REVERT: A 1003 MET cc_start: 0.6491 (tpp) cc_final: 0.6199 (tpp) REVERT: A 1378 LEU cc_start: 0.7270 (mt) cc_final: 0.6834 (mp) outliers start: 13 outliers final: 9 residues processed: 46 average time/residue: 0.0325 time to fit residues: 2.2637 Evaluate side-chains 48 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 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 962 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.0020 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 40 optimal weight: 8.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.129868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.106477 restraints weight = 11894.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.108779 restraints weight = 7146.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.110474 restraints weight = 5086.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.111302 restraints weight = 4054.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.112211 restraints weight = 3560.455| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4263 Z= 0.128 Angle : 0.979 35.716 5959 Z= 0.343 Chirality : 0.041 0.274 656 Planarity : 0.004 0.032 604 Dihedral : 27.328 175.640 899 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.86 % Allowed : 18.00 % Favored : 79.14 % 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: -0.74 (0.45), residues: 383 helix: 1.19 (0.41), residues: 172 sheet: -3.70 (0.79), residues: 22 loop : -1.74 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1221 TYR 0.010 0.001 TYR A1001 PHE 0.009 0.001 PHE A1033 TRP 0.013 0.001 TRP A 562 HIS 0.002 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 4256) covalent geometry : angle 0.62955 / 0.34 ( 5947) hydrogen bonds : bond 0.04568 / 3.06 ( 167) hydrogen bonds : angle 5.11273 / 3.61 ( 433) metal coordination : bond 0.00914 / 0.46 ( 4) metal coordination : angle 16.71115 / 9.64 ( 12) Misc. bond : bond 0.00045 / 0.02 ( 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 56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 562 TRP cc_start: 0.6371 (t-100) cc_final: 0.5705 (t60) REVERT: A 619 MET cc_start: 0.8529 (mtp) cc_final: 0.8310 (mtm) REVERT: A 905 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7110 (mtt) REVERT: A 1378 LEU cc_start: 0.7151 (mt) cc_final: 0.6730 (mp) outliers start: 10 outliers final: 9 residues processed: 52 average time/residue: 0.0383 time to fit residues: 3.0089 Evaluate side-chains 50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4116 r_free = 0.4116 target = 0.128992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104732 restraints weight = 12290.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107239 restraints weight = 7377.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.108942 restraints weight = 5209.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.110102 restraints weight = 4166.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.110810 restraints weight = 3591.738| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4263 Z= 0.130 Angle : 0.977 35.024 5959 Z= 0.351 Chirality : 0.042 0.266 656 Planarity : 0.004 0.033 604 Dihedral : 27.260 175.666 899 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.57 % Allowed : 18.86 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.45), residues: 383 helix: 1.13 (0.41), residues: 172 sheet: -3.69 (0.80), residues: 22 loop : -1.61 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1221 TYR 0.014 0.002 TYR A1300 PHE 0.011 0.001 PHE A1033 TRP 0.012 0.001 TRP A 562 HIS 0.002 0.001 HIS A1056 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 4256) covalent geometry : angle 0.65275 / 0.35 ( 5947) hydrogen bonds : bond 0.04603 / 3.06 ( 167) hydrogen bonds : angle 5.19555 / 3.70 ( 433) metal coordination : bond 0.00807 / 0.40 ( 4) metal coordination : angle 16.21224 / 9.38 ( 12) Misc. bond : bond 0.00049 / 0.02 ( 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 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 562 TRP cc_start: 0.6591 (t-100) cc_final: 0.5855 (t60) REVERT: A 1378 LEU cc_start: 0.7236 (mt) cc_final: 0.6817 (mp) outliers start: 9 outliers final: 8 residues processed: 49 average time/residue: 0.0358 time to fit residues: 2.6926 Evaluate side-chains 48 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.2980 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4125 r_free = 0.4125 target = 0.129703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.105232 restraints weight = 12071.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107781 restraints weight = 7309.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.109510 restraints weight = 5215.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.110490 restraints weight = 4160.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.111296 restraints weight = 3626.389| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4263 Z= 0.127 Angle : 0.956 33.748 5959 Z= 0.349 Chirality : 0.042 0.260 656 Planarity : 0.005 0.034 604 Dihedral : 27.212 174.895 899 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.29 % Allowed : 19.14 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.45), residues: 383 helix: 1.12 (0.41), residues: 172 sheet: -3.71 (0.80), residues: 22 loop : -1.54 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1287 TYR 0.010 0.001 TYR A1028 PHE 0.011 0.001 PHE A 569 TRP 0.013 0.001 TRP A 562 HIS 0.002 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 4256) covalent geometry : angle 0.65056 / 0.34 ( 5947) hydrogen bonds : bond 0.04366 / 2.95 ( 167) hydrogen bonds : angle 5.04508 / 3.58 ( 433) metal coordination : bond 0.00726 / 0.36 ( 4) metal coordination : angle 15.63416 / 9.06 ( 12) Misc. bond : bond 0.00049 / 0.02 ( 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 53 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 562 TRP cc_start: 0.6623 (t-100) cc_final: 0.5893 (t60) REVERT: A 942 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8207 (tm-30) outliers start: 8 outliers final: 7 residues processed: 50 average time/residue: 0.0454 time to fit residues: 3.2520 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 : 0.118 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4117 r_free = 0.4117 target = 0.128890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.105302 restraints weight = 12233.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107568 restraints weight = 7496.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.109370 restraints weight = 5427.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.110510 restraints weight = 4336.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.111119 restraints weight = 3726.312| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2972 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= 0.134 Angle : 0.958 33.769 5959 Z= 0.350 Chirality : 0.043 0.259 656 Planarity : 0.005 0.033 604 Dihedral : 27.211 174.869 899 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.00 % Allowed : 20.57 % 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: -0.69 (0.45), residues: 383 helix: 1.13 (0.41), residues: 172 sheet: -3.87 (0.81), residues: 22 loop : -1.57 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1221 TYR 0.010 0.001 TYR A1028 PHE 0.011 0.001 PHE A1342 TRP 0.013 0.001 TRP A1012 HIS 0.006 0.001 HIS A1203 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 4256) covalent geometry : angle 0.65517 / 0.34 ( 5947) hydrogen bonds : bond 0.04418 / 2.95 ( 167) hydrogen bonds : angle 5.11628 / 3.65 ( 433) metal coordination : bond 0.00824 / 0.41 ( 4) metal coordination : angle 15.58248 / 9.05 ( 12) Misc. bond : bond 0.00059 / 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 50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 562 TRP cc_start: 0.6527 (t-100) cc_final: 0.5844 (t60) REVERT: A 942 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8143 (tm-30) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.0348 time to fit residues: 2.3829 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 : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4109 r_free = 0.4109 target = 0.128303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104654 restraints weight = 11939.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107108 restraints weight = 7165.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.108836 restraints weight = 5082.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.109946 restraints weight = 4036.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.110630 restraints weight = 3475.224| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4263 Z= 0.137 Angle : 0.958 33.790 5959 Z= 0.350 Chirality : 0.043 0.256 656 Planarity : 0.005 0.034 604 Dihedral : 27.230 174.250 898 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.57 % Allowed : 20.00 % 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: -0.70 (0.45), residues: 383 helix: 1.08 (0.41), residues: 173 sheet: -3.61 (0.82), residues: 22 loop : -1.59 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1221 TYR 0.010 0.001 TYR A1028 PHE 0.014 0.001 PHE A1334 TRP 0.011 0.001 TRP A 562 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 4256) covalent geometry : angle 0.65550 / 0.34 ( 5947) hydrogen bonds : bond 0.04452 / 2.93 ( 167) hydrogen bonds : angle 5.02508 / 3.57 ( 433) metal coordination : bond 0.00830 / 0.41 ( 4) metal coordination : angle 15.57722 / 9.06 ( 12) Misc. bond : bond 0.00060 / 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 52 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 562 TRP cc_start: 0.6599 (t-100) cc_final: 0.5884 (t60) REVERT: A 942 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8163 (tm-30) outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 0.0436 time to fit residues: 3.0104 Evaluate side-chains 50 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.0000 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4117 r_free = 0.4117 target = 0.128802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104865 restraints weight = 11969.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.107278 restraints weight = 7286.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.109063 restraints weight = 5231.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.110207 restraints weight = 4179.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.110943 restraints weight = 3598.753| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4263 Z= 0.127 Angle : 0.944 32.807 5959 Z= 0.349 Chirality : 0.043 0.263 656 Planarity : 0.005 0.034 604 Dihedral : 27.239 173.602 898 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.71 % Allowed : 20.86 % 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: -0.65 (0.45), residues: 383 helix: 1.06 (0.41), residues: 179 sheet: -3.65 (0.81), residues: 22 loop : -1.56 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1287 TYR 0.009 0.001 TYR A1028 PHE 0.010 0.001 PHE A1334 TRP 0.021 0.001 TRP A1012 HIS 0.002 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 ( 4256) covalent geometry : angle 0.65694 / 0.34 ( 5947) hydrogen bonds : bond 0.04200 / 2.81 ( 167) hydrogen bonds : angle 5.03628 / 3.61 ( 433) metal coordination : bond 0.00702 / 0.35 ( 4) metal coordination : angle 15.11910 / 8.78 ( 12) Misc. bond : bond 0.00056 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 894.54 seconds wall clock time: 16 minutes 7.45 seconds (967.45 seconds total)