Starting phenix.real_space_refine on Thu Jul 2 11:57:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ky4_62637/07_2026/9ky4_62637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ky4_62637/07_2026/9ky4_62637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ky4_62637/07_2026/9ky4_62637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ky4_62637/07_2026/9ky4_62637.map" model { file = "/net/cci-nas-00/data/ceres_data/9ky4_62637/07_2026/9ky4_62637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ky4_62637/07_2026/9ky4_62637.cif" } resolution = 3.0 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1750 atoms to isotropic. 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 Zn 1 6.06 5 P 66 5.49 5 S 20 5.16 5 C 4186 2.51 5 N 1271 2.21 5 O 1459 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: 7003 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4664 Classifications: {'peptide': 638} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 602} Chain: "B" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 666 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 687 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 985 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 13, 'TRANS': 120} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6638 SG CYS D1373 42.156 43.574 106.145 1.00 30.00 S ATOM 6659 SG CYS D1376 44.778 45.141 107.531 1.00 66.19 S Time building chain proxies: 1.76, per 1000 atoms: 0.25 Number of scatterers: 7003 At special positions: 0 Unit cell: (83.8941, 82.9298, 134.038, 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) Zn 1 29.99 S 20 16.00 P 66 15.00 O 1459 8.00 N 1271 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 379.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D1373 " pdb="ZN ZN D1501 " - pdb=" ND1 HIS D1345 " pdb="ZN ZN D1501 " - pdb=" SG CYS D1376 " 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 1 sheets defined 70.7% alpha, 0.5% beta 8 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 37 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.690A pdb=" N THR A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 83 through 99 removed outlier: 3.972A pdb=" N THR A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 155 through 170 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 186 through 204 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 223 through 238 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 254 through 272 Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 288 through 307 Proline residue: A 301 - end of helix removed outlier: 3.516A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.631A pdb=" N ALA A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.591A pdb=" N ALA A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.642A pdb=" N HIS A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 387 Processing helix chain 'A' and resid 390 through 409 removed outlier: 3.566A pdb=" N ARG A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix removed outlier: 3.616A pdb=" N HIS A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 424 through 443 removed outlier: 3.710A pdb=" N ALA A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.685A pdb=" N HIS A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 Processing helix chain 'A' and resid 458 through 477 Proline residue: A 471 - end of helix removed outlier: 3.559A pdb=" N HIS A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 removed outlier: 4.431A pdb=" N HIS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 511 Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 526 through 544 Proline residue: A 539 - end of helix Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 560 through 579 Proline residue: A 573 - end of helix Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 594 through 612 Proline residue: A 607 - end of helix Processing helix chain 'A' and resid 616 through 625 Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.691A pdb=" N ALA A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 1340 through 1345 Processing helix chain 'D' and resid 1346 through 1349 removed outlier: 3.505A pdb=" N GLN D1349 " --> pdb=" O VAL D1346 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1346 through 1349' Processing helix chain 'D' and resid 1350 through 1355 Processing sheet with id=AA1, first strand: chain 'D' and resid 1313 through 1315 removed outlier: 3.633A pdb=" N PHE D1365 " --> pdb=" O THR D1314 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1652 1.33 - 1.45: 1568 1.45 - 1.57: 3886 1.57 - 1.69: 130 1.69 - 1.81: 24 Bond restraints: 7260 Sorted by residual: bond pdb=" C3' DC C 18 " pdb=" C2' DC C 18 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.45e+01 bond pdb=" C3' DG C 19 " pdb=" C2' DG C 19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.50e+00 bond pdb=" C3' DG B 10 " pdb=" C2' DG B 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.99e+00 bond pdb=" C3' DC C 21 " pdb=" C2' DC C 21 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.58e+00 bond pdb=" C3' DT C 14 " pdb=" C2' DT C 14 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.96e+00 ... (remaining 7255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 9953 2.20 - 4.40: 188 4.40 - 6.60: 24 6.60 - 8.79: 5 8.79 - 10.99: 1 Bond angle restraints: 10171 Sorted by residual: angle pdb=" N PHE D1375 " pdb=" CA PHE D1375 " pdb=" C PHE D1375 " ideal model delta sigma weight residual 112.89 105.94 6.95 1.24e+00 6.50e-01 3.14e+01 angle pdb=" C HIS D1345 " pdb=" CA HIS D1345 " pdb=" CB HIS D1345 " ideal model delta sigma weight residual 110.40 121.39 -10.99 2.07e+00 2.33e-01 2.82e+01 angle pdb=" CA THR D1372 " pdb=" CB THR D1372 " pdb=" OG1 THR D1372 " ideal model delta sigma weight residual 109.60 102.31 7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" N3 DT C 22 " pdb=" C4 DT C 22 " pdb=" O4 DT C 22 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT B 20 " pdb=" C4 DT B 20 " pdb=" O4 DT B 20 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 10166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.28: 3748 30.28 - 60.56: 434 60.56 - 90.85: 13 90.85 - 121.13: 1 121.13 - 151.41: 5 Dihedral angle restraints: 4201 sinusoidal: 2038 harmonic: 2163 Sorted by residual: dihedral pdb=" CA ILE D1413 " pdb=" C ILE D1413 " pdb=" N GLY D1414 " pdb=" CA GLY D1414 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" C4' DG C 25 " pdb=" C3' DG C 25 " pdb=" O3' DG C 25 " pdb=" P DC C 26 " ideal model delta sinusoidal sigma weight residual 220.00 68.59 151.41 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" C4' DA C 17 " pdb=" C3' DA C 17 " pdb=" O3' DA C 17 " pdb=" P DC C 18 " ideal model delta sinusoidal sigma weight residual 220.00 69.09 150.91 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 4198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 693 0.029 - 0.058: 308 0.058 - 0.088: 121 0.088 - 0.117: 80 0.117 - 0.146: 8 Chirality restraints: 1210 Sorted by residual: chirality pdb=" CA HIS D1345 " pdb=" N HIS D1345 " pdb=" C HIS D1345 " pdb=" CB HIS D1345 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" P DC C 26 " pdb=" OP1 DC C 26 " pdb=" OP2 DC C 26 " pdb=" O5' DC C 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.46 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" C3' DG C 19 " pdb=" C4' DG C 19 " pdb=" O3' DG C 19 " pdb=" C2' DG C 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.61 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1207 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D1418 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO D1419 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D1419 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D1419 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D1353 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C PHE D1353 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE D1353 " 0.015 2.00e-02 2.50e+03 pdb=" N MET D1354 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 242 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 243 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.027 5.00e-02 4.00e+02 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 583 2.74 - 3.28: 6376 3.28 - 3.82: 11031 3.82 - 4.36: 12893 4.36 - 4.90: 22406 Nonbonded interactions: 53289 Sorted by model distance: nonbonded pdb=" OG1 THR A 616 " pdb=" OE1 GLN A 619 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN D1415 " pdb=" N SER D1416 " model vdw 2.200 3.120 nonbonded pdb=" OG1 THR A 208 " pdb=" OE1 GLU A 210 " model vdw 2.206 3.040 nonbonded pdb=" N GLU A 516 " pdb=" OE1 GLU A 516 " model vdw 2.242 3.120 nonbonded pdb=" O VAL A 417 " pdb=" OG SER A 421 " model vdw 2.252 3.040 ... (remaining 53284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.590 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 7263 Z= 0.375 Angle : 0.707 10.992 10171 Z= 0.513 Chirality : 0.043 0.146 1210 Planarity : 0.005 0.070 1104 Dihedral : 22.145 151.408 2817 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.67 % Allowed : 18.14 % Favored : 81.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 4.17 % 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 (0.30), residues: 768 helix: 0.48 (0.24), residues: 490 sheet: 0.39 (1.69), residues: 12 loop : -2.49 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.007 0.001 TYR D1316 PHE 0.009 0.001 PHE D1412 TRP 0.004 0.001 TRP A 128 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.35 ( 7260) covalent geometry : angle 0.70673 / 0.51 (10171) hydrogen bonds : bond 0.17139 / 11.58 ( 328) hydrogen bonds : angle 5.49975 / 4.06 ( 955) metal coordination : bond 0.20344 / 10.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.237 Fit side-chains REVERT: A 196 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7482 (ttm170) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.5946 time to fit residues: 45.6897 Evaluate side-chains 69 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain D residue 1375 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.0370 chunk 74 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN A 341 HIS D1339 ASN D1357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109449 restraints weight = 10980.792| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.59 r_work: 0.3292 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7263 Z= 0.197 Angle : 0.649 7.137 10171 Z= 0.363 Chirality : 0.046 0.204 1210 Planarity : 0.006 0.072 1104 Dihedral : 24.391 155.819 1529 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.33 % Allowed : 15.97 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.85 (0.30), residues: 768 helix: 0.55 (0.23), residues: 508 sheet: -0.21 (1.53), residues: 14 loop : -3.04 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.009 0.001 TYR D1316 PHE 0.006 0.001 PHE D1412 TRP 0.008 0.002 TRP A 128 HIS 0.007 0.001 HIS D1345 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 ( 7260) covalent geometry : angle 0.64860 / 0.36 (10171) hydrogen bonds : bond 0.05910 / 4.00 ( 328) hydrogen bonds : angle 4.70346 / 3.41 ( 955) metal coordination : bond 0.02257 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.246 Fit side-chains REVERT: A 17 LYS cc_start: 0.8215 (tppp) cc_final: 0.7917 (ttpp) REVERT: A 300 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7969 (tp) outliers start: 20 outliers final: 11 residues processed: 83 average time/residue: 0.5346 time to fit residues: 46.9646 Evaluate side-chains 81 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain D residue 1299 ILE Chi-restraints excluded: chain D residue 1326 SER Chi-restraints excluded: chain D residue 1339 ASN Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1378 ASN Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1391 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110050 restraints weight = 10880.184| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.46 r_work: 0.3307 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7263 Z= 0.176 Angle : 0.636 8.090 10171 Z= 0.353 Chirality : 0.045 0.221 1210 Planarity : 0.005 0.047 1104 Dihedral : 24.442 158.059 1523 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.66 % Allowed : 17.47 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.80 (0.30), residues: 768 helix: 0.61 (0.23), residues: 508 sheet: -0.47 (1.53), residues: 14 loop : -3.04 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.008 0.001 TYR D1340 PHE 0.009 0.001 PHE D1412 TRP 0.008 0.002 TRP A 128 HIS 0.005 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 ( 7260) covalent geometry : angle 0.63589 / 0.35 (10171) hydrogen bonds : bond 0.05078 / 3.46 ( 328) hydrogen bonds : angle 4.54801 / 3.29 ( 955) metal coordination : bond 0.00847 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.206 Fit side-chains REVERT: A 17 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7878 (ttpp) REVERT: A 176 GLU cc_start: 0.7414 (mp0) cc_final: 0.7068 (mp0) outliers start: 22 outliers final: 14 residues processed: 87 average time/residue: 0.5049 time to fit residues: 46.4498 Evaluate side-chains 87 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain D residue 1299 ILE Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1378 ASN Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1391 THR Chi-restraints excluded: chain D residue 1413 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 50 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110551 restraints weight = 10942.551| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.48 r_work: 0.3315 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7263 Z= 0.153 Angle : 0.606 7.288 10171 Z= 0.336 Chirality : 0.044 0.224 1210 Planarity : 0.005 0.047 1104 Dihedral : 24.522 159.781 1523 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.16 % Allowed : 16.64 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.76 (0.30), residues: 768 helix: 0.64 (0.23), residues: 508 sheet: -0.40 (1.51), residues: 14 loop : -3.01 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 99 TYR 0.006 0.001 TYR D1316 PHE 0.009 0.001 PHE D1412 TRP 0.007 0.001 TRP A 128 HIS 0.006 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 7260) covalent geometry : angle 0.60574 / 0.34 (10171) hydrogen bonds : bond 0.04453 / 3.05 ( 328) hydrogen bonds : angle 4.43889 / 3.21 ( 955) metal coordination : bond 0.00540 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.152 Fit side-chains REVERT: A 17 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7897 (ttpp) REVERT: A 300 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7963 (tp) outliers start: 25 outliers final: 16 residues processed: 89 average time/residue: 0.4376 time to fit residues: 41.4117 Evaluate side-chains 86 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain D residue 1299 ILE Chi-restraints excluded: chain D residue 1326 SER Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1378 ASN Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1391 THR Chi-restraints excluded: chain D residue 1413 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109473 restraints weight = 10927.984| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.47 r_work: 0.3297 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7263 Z= 0.183 Angle : 0.641 7.945 10171 Z= 0.352 Chirality : 0.046 0.240 1210 Planarity : 0.005 0.047 1104 Dihedral : 24.594 159.648 1523 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.66 % Allowed : 16.81 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.30), residues: 768 helix: 0.64 (0.23), residues: 508 sheet: 1.01 (1.53), residues: 12 loop : -3.07 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.008 0.001 TYR D1316 PHE 0.010 0.001 PHE D1412 TRP 0.006 0.002 TRP A 128 HIS 0.007 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 7260) covalent geometry : angle 0.64091 / 0.35 (10171) hydrogen bonds : bond 0.04986 / 3.43 ( 328) hydrogen bonds : angle 4.46376 / 3.21 ( 955) metal coordination : bond 0.00808 / 0.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.231 Fit side-chains REVERT: A 6 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7824 (mmm160) REVERT: A 17 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7875 (ttpp) REVERT: A 278 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: A 436 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7898 (tp) outliers start: 28 outliers final: 17 residues processed: 91 average time/residue: 0.4631 time to fit residues: 44.7127 Evaluate side-chains 89 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain D residue 1299 ILE Chi-restraints excluded: chain D residue 1326 SER Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1378 ASN Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1413 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108394 restraints weight = 10920.239| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.48 r_work: 0.3276 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7263 Z= 0.218 Angle : 0.678 7.772 10171 Z= 0.369 Chirality : 0.048 0.247 1210 Planarity : 0.005 0.049 1104 Dihedral : 24.635 159.980 1523 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.99 % Allowed : 17.80 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.81 (0.30), residues: 768 helix: 0.57 (0.23), residues: 513 sheet: 1.10 (1.53), residues: 12 loop : -3.11 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.006 0.001 TYR D1317 PHE 0.011 0.001 PHE D1412 TRP 0.006 0.002 TRP A 128 HIS 0.006 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 ( 7260) covalent geometry : angle 0.67751 / 0.37 (10171) hydrogen bonds : bond 0.05408 / 3.72 ( 328) hydrogen bonds : angle 4.52336 / 3.25 ( 955) metal coordination : bond 0.01024 / 0.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7806 (mmm160) REVERT: A 17 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7882 (ttpp) REVERT: A 278 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: A 436 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7901 (tp) REVERT: A 634 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6900 (tm-30) outliers start: 24 outliers final: 20 residues processed: 87 average time/residue: 0.5378 time to fit residues: 49.3967 Evaluate side-chains 92 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain D residue 1299 ILE Chi-restraints excluded: chain D residue 1325 GLU Chi-restraints excluded: chain D residue 1326 SER Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1378 ASN Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 0.0670 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN A 511 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109557 restraints weight = 10816.308| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.47 r_work: 0.3296 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7263 Z= 0.169 Angle : 0.644 8.107 10171 Z= 0.352 Chirality : 0.046 0.238 1210 Planarity : 0.005 0.049 1104 Dihedral : 24.653 161.134 1523 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.33 % Allowed : 18.47 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.30), residues: 768 helix: 0.60 (0.23), residues: 513 sheet: 1.36 (1.54), residues: 12 loop : -3.13 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 99 TYR 0.009 0.001 TYR D1316 PHE 0.014 0.001 PHE D1412 TRP 0.006 0.002 TRP A 128 HIS 0.006 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 7260) covalent geometry : angle 0.64415 / 0.35 (10171) hydrogen bonds : bond 0.04634 / 3.19 ( 328) hydrogen bonds : angle 4.45274 / 3.20 ( 955) metal coordination : bond 0.00656 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.182 Fit side-chains REVERT: A 6 ARG cc_start: 0.8167 (mmm160) cc_final: 0.7775 (mmm160) REVERT: A 17 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7911 (ttpp) REVERT: A 61 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7261 (mm-40) outliers start: 26 outliers final: 18 residues processed: 88 average time/residue: 0.4659 time to fit residues: 43.5206 Evaluate side-chains 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain D residue 1299 ILE Chi-restraints excluded: chain D residue 1326 SER Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1364 VAL Chi-restraints excluded: chain D residue 1378 ASN Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN A 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108330 restraints weight = 10885.510| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.49 r_work: 0.3278 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7263 Z= 0.202 Angle : 0.675 8.324 10171 Z= 0.367 Chirality : 0.047 0.250 1210 Planarity : 0.005 0.049 1104 Dihedral : 24.677 160.785 1523 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.99 % Allowed : 19.47 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.83 (0.30), residues: 768 helix: 0.57 (0.23), residues: 513 sheet: 1.46 (1.59), residues: 12 loop : -3.18 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.008 0.001 TYR D1316 PHE 0.013 0.001 PHE D1412 TRP 0.005 0.002 TRP A 128 HIS 0.007 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 ( 7260) covalent geometry : angle 0.67533 / 0.37 (10171) hydrogen bonds : bond 0.05172 / 3.56 ( 328) hydrogen bonds : angle 4.49939 / 3.23 ( 955) metal coordination : bond 0.00885 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7768 (mmm160) REVERT: A 17 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7891 (ttpp) REVERT: A 278 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: A 436 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7825 (tt) REVERT: D 1349 GLN cc_start: 0.7326 (mp10) cc_final: 0.6971 (mt0) outliers start: 24 outliers final: 21 residues processed: 86 average time/residue: 0.4832 time to fit residues: 43.8904 Evaluate side-chains 92 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain D residue 1299 ILE Chi-restraints excluded: chain D residue 1325 GLU Chi-restraints excluded: chain D residue 1326 SER Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1364 VAL Chi-restraints excluded: chain D residue 1375 PHE Chi-restraints excluded: chain D residue 1378 ASN Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 26 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109519 restraints weight = 10800.033| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.47 r_work: 0.3297 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7263 Z= 0.165 Angle : 0.652 9.458 10171 Z= 0.354 Chirality : 0.045 0.239 1210 Planarity : 0.005 0.049 1104 Dihedral : 24.699 162.120 1523 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.83 % Allowed : 19.80 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.71 (0.30), residues: 768 helix: 0.68 (0.23), residues: 511 sheet: 1.81 (1.66), residues: 12 loop : -3.15 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.007 0.001 TYR D1316 PHE 0.005 0.001 PHE D1412 TRP 0.007 0.001 TRP A 128 HIS 0.006 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 7260) covalent geometry : angle 0.65214 / 0.35 (10171) hydrogen bonds : bond 0.04558 / 3.14 ( 328) hydrogen bonds : angle 4.44172 / 3.19 ( 955) metal coordination : bond 0.00624 / 0.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7773 (mmm160) REVERT: A 17 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7908 (ttpp) REVERT: A 436 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7845 (tt) REVERT: A 634 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6978 (tm-30) REVERT: D 1349 GLN cc_start: 0.7283 (mp10) cc_final: 0.6933 (mt0) outliers start: 23 outliers final: 18 residues processed: 86 average time/residue: 0.5247 time to fit residues: 47.7442 Evaluate side-chains 89 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain D residue 1299 ILE Chi-restraints excluded: chain D residue 1325 GLU Chi-restraints excluded: chain D residue 1326 SER Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1378 ASN Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 43 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110923 restraints weight = 10712.504| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.46 r_work: 0.3316 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7263 Z= 0.141 Angle : 0.624 10.464 10171 Z= 0.339 Chirality : 0.044 0.234 1210 Planarity : 0.005 0.049 1104 Dihedral : 24.735 163.728 1523 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.33 % Allowed : 20.13 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.55 (0.30), residues: 768 helix: 0.78 (0.23), residues: 510 sheet: 2.11 (1.61), residues: 12 loop : -3.05 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1355 TYR 0.010 0.001 TYR D1316 PHE 0.011 0.001 PHE D1412 TRP 0.007 0.001 TRP A 128 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 7260) covalent geometry : angle 0.62409 / 0.34 (10171) hydrogen bonds : bond 0.03990 / 2.75 ( 328) hydrogen bonds : angle 4.35588 / 3.13 ( 955) metal coordination : bond 0.00428 / 0.21 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.186 Fit side-chains REVERT: A 5 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7754 (tp) REVERT: A 6 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7770 (mmm160) REVERT: A 17 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7908 (ttpp) REVERT: A 19 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8226 (mmtm) REVERT: A 61 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7256 (mm-40) REVERT: A 436 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7795 (tt) REVERT: A 634 GLU cc_start: 0.7475 (tm-30) cc_final: 0.6948 (tm-30) REVERT: D 1349 GLN cc_start: 0.7143 (mp10) cc_final: 0.6864 (mt0) outliers start: 20 outliers final: 18 residues processed: 83 average time/residue: 0.5070 time to fit residues: 44.6226 Evaluate side-chains 89 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain D residue 1299 ILE Chi-restraints excluded: chain D residue 1318 VAL Chi-restraints excluded: chain D residue 1326 SER Chi-restraints excluded: chain D residue 1335 THR Chi-restraints excluded: chain D residue 1378 ASN Chi-restraints excluded: chain D residue 1384 LEU Chi-restraints excluded: chain D residue 1413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110441 restraints weight = 10669.461| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.46 r_work: 0.3310 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7263 Z= 0.155 Angle : 0.640 10.132 10171 Z= 0.346 Chirality : 0.044 0.243 1210 Planarity : 0.005 0.048 1104 Dihedral : 24.741 163.547 1523 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.16 % Allowed : 20.30 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.30), residues: 768 helix: 0.72 (0.23), residues: 512 sheet: 2.11 (1.64), residues: 12 loop : -3.14 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1355 TYR 0.007 0.001 TYR D1316 PHE 0.009 0.001 PHE D1412 TRP 0.006 0.001 TRP A 128 HIS 0.006 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 7260) covalent geometry : angle 0.63954 / 0.35 (10171) hydrogen bonds : bond 0.04261 / 2.93 ( 328) hydrogen bonds : angle 4.36019 / 3.13 ( 955) metal coordination : bond 0.00540 / 0.26 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.45 seconds wall clock time: 36 minutes 2.03 seconds (2162.03 seconds total)