Starting phenix.real_space_refine on Wed Feb 4 02:43:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ky4_62637/02_2026/9ky4_62637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ky4_62637/02_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_62637/02_2026/9ky4_62637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ky4_62637/02_2026/9ky4_62637.map" model { file = "/net/cci-nas-00/data/ceres_data/9ky4_62637/02_2026/9ky4_62637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ky4_62637/02_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-2.0-5952/lib/python3.9/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: 1.54, per 1000 atoms: 0.22 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: 0.62 Conformation dependent library (CDL) restraints added in 159.0 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: 0.65 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: 1.18 Time building geometry restraints manager: 0.78 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=" C ASN D1417 " pdb=" N SER D1418 " ideal model delta sigma weight residual 1.331 1.385 -0.054 2.07e-02 2.33e+03 6.73e+00 bond pdb=" N CYS D1373 " pdb=" CA CYS D1373 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.25e-02 6.40e+03 3.40e+00 bond pdb=" N HIS D1345 " pdb=" CA HIS D1345 " ideal model delta sigma weight residual 1.453 1.475 -0.023 1.31e-02 5.83e+03 2.98e+00 bond pdb=" CG HIS D1345 " pdb=" CD2 HIS D1345 " ideal model delta sigma weight residual 1.354 1.335 0.019 1.10e-02 8.26e+03 2.85e+00 bond pdb=" CA PHE D1375 " pdb=" C PHE D1375 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.39e-02 5.18e+03 2.58e+00 ... (remaining 7255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 10012 2.20 - 4.40: 129 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=" N HIS D1345 " pdb=" CA HIS D1345 " pdb=" C HIS D1345 " ideal model delta sigma weight residual 110.53 105.59 4.94 1.29e+00 6.01e-01 1.47e+01 angle pdb=" CB HIS D1345 " pdb=" CG HIS D1345 " pdb=" CD2 HIS D1345 " ideal model delta sigma weight residual 131.20 136.17 -4.97 1.30e+00 5.92e-01 1.46e+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: 753 0.029 - 0.058: 298 0.058 - 0.088: 91 0.088 - 0.117: 66 0.117 - 0.146: 2 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=" CA PRO A 68 " pdb=" N PRO A 68 " pdb=" C PRO A 68 " pdb=" CB PRO A 68 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.46e-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 2.35 -2.46 -0.12 2.00e-01 2.50e+01 3.41e-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: 3.160 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.620 Find NCS groups from input model: 0.020 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:5.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.005 0.241 7263 Z= 0.212 Angle : 0.633 10.992 10171 Z= 0.349 Chirality : 0.039 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 covalent geometry : bond 0.00339 ( 7260) covalent geometry : angle 0.63256 (10171) hydrogen bonds : bond 0.17139 ( 328) hydrogen bonds : angle 5.49975 ( 955) metal coordination : bond 0.20344 ( 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 : 0.194 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: 0.5131 time to fit residues: 39.5145 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 : 0.267 ------------------------------------------------------------------------------- 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: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.0370 chunk 74 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3588 r_free = 0.3588 target = 0.122099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109453 restraints weight = 11029.441| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.51 r_work: 0.3296 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7263 Z= 0.204 Angle : 0.620 7.379 10171 Z= 0.339 Chirality : 0.042 0.126 1210 Planarity : 0.006 0.053 1104 Dihedral : 24.276 152.560 1529 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.00 % Allowed : 16.31 % 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: -0.81 (0.30), residues: 768 helix: 0.54 (0.23), residues: 513 sheet: -0.12 (1.53), residues: 14 loop : -2.97 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.007 0.001 TYR D1316 PHE 0.008 0.001 PHE D1412 TRP 0.009 0.002 TRP A 128 HIS 0.007 0.001 HIS D1345 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 7260) covalent geometry : angle 0.62034 (10171) hydrogen bonds : bond 0.05228 ( 328) hydrogen bonds : angle 4.54907 ( 955) metal coordination : bond 0.00331 ( 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 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.221 Fit side-chains REVERT: A 17 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7897 (ttpp) REVERT: A 300 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7945 (tp) outliers start: 18 outliers final: 10 residues processed: 83 average time/residue: 0.4755 time to fit residues: 41.6844 Evaluate side-chains 79 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110572 restraints weight = 10925.689| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.49 r_work: 0.3310 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1062 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= 0.165 Angle : 0.592 7.905 10171 Z= 0.321 Chirality : 0.040 0.131 1210 Planarity : 0.005 0.048 1104 Dihedral : 24.216 154.865 1523 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.83 % Allowed : 16.31 % Favored : 79.87 % 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: -0.75 (0.30), residues: 768 helix: 0.60 (0.23), residues: 513 sheet: -0.14 (1.55), residues: 14 loop : -2.99 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 0.005 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7260) covalent geometry : angle 0.59155 (10171) hydrogen bonds : bond 0.04380 ( 328) hydrogen bonds : angle 4.41516 ( 955) metal coordination : bond 0.00636 ( 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 97 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.187 Fit side-chains REVERT: A 17 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7874 (ttpp) REVERT: A 176 GLU cc_start: 0.7461 (mp0) cc_final: 0.7116 (mp0) REVERT: A 210 GLU cc_start: 0.7691 (mp0) cc_final: 0.7459 (mp0) REVERT: A 300 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7911 (tp) outliers start: 23 outliers final: 14 residues processed: 87 average time/residue: 0.4803 time to fit residues: 44.2837 Evaluate side-chains 87 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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 1391 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109832 restraints weight = 10890.385| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.58 r_work: 0.3296 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7263 Z= 0.167 Angle : 0.590 7.582 10171 Z= 0.320 Chirality : 0.040 0.121 1210 Planarity : 0.005 0.048 1104 Dihedral : 24.227 156.435 1523 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.66 % Allowed : 16.31 % Favored : 79.03 % 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: -0.63 (0.30), residues: 768 helix: 0.67 (0.23), residues: 513 sheet: 1.23 (1.58), residues: 12 loop : -2.96 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 400 TYR 0.006 0.001 TYR D1316 PHE 0.010 0.001 PHE D1412 TRP 0.006 0.001 TRP A 128 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7260) covalent geometry : angle 0.59030 (10171) hydrogen bonds : bond 0.04326 ( 328) hydrogen bonds : angle 4.37403 ( 955) metal coordination : bond 0.00578 ( 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: 28 poor density : 68 time to evaluate : 0.230 Fit side-chains REVERT: A 17 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7904 (ttpp) REVERT: A 300 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7945 (tp) REVERT: A 634 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6888 (tm-30) outliers start: 28 outliers final: 16 residues processed: 87 average time/residue: 0.4649 time to fit residues: 42.9693 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 : 0.165 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 0.0040 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 overall best weight: 0.2210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112768 restraints weight = 10917.129| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.49 r_work: 0.3347 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7263 Z= 0.130 Angle : 0.569 7.574 10171 Z= 0.306 Chirality : 0.039 0.149 1210 Planarity : 0.005 0.047 1104 Dihedral : 24.193 157.593 1523 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.99 % Allowed : 16.97 % Favored : 79.03 % 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: -0.41 (0.30), residues: 768 helix: 0.85 (0.23), residues: 512 sheet: 1.21 (1.52), residues: 12 loop : -2.86 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 604 TYR 0.015 0.001 TYR D1316 PHE 0.010 0.001 PHE D1412 TRP 0.006 0.001 TRP A 128 HIS 0.004 0.000 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7260) covalent geometry : angle 0.56853 (10171) hydrogen bonds : bond 0.03313 ( 328) hydrogen bonds : angle 4.23392 ( 955) metal coordination : bond 0.00302 ( 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 93 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.146 Fit side-chains REVERT: A 17 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7996 (ttpp) REVERT: A 19 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8146 (mmtm) REVERT: A 300 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7965 (tp) REVERT: A 414 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: D 1324 LEU cc_start: 0.2363 (OUTLIER) cc_final: 0.0554 (pp) REVERT: D 1349 GLN cc_start: 0.7278 (mp10) cc_final: 0.7004 (mt0) outliers start: 24 outliers final: 15 residues processed: 85 average time/residue: 0.4637 time to fit residues: 41.7740 Evaluate side-chains 83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 GLU 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 D residue 1299 ILE Chi-restraints excluded: chain D residue 1324 LEU Chi-restraints excluded: chain D residue 1359 ILE 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: 0.9990 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 26 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111223 restraints weight = 10867.665| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.47 r_work: 0.3327 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7263 Z= 0.151 Angle : 0.578 7.378 10171 Z= 0.311 Chirality : 0.039 0.121 1210 Planarity : 0.005 0.046 1104 Dihedral : 24.199 157.295 1523 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.33 % Allowed : 16.64 % Favored : 79.03 % 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: -0.43 (0.30), residues: 768 helix: 0.83 (0.23), residues: 512 sheet: 1.33 (1.50), residues: 12 loop : -2.87 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 604 TYR 0.007 0.001 TYR D1316 PHE 0.010 0.001 PHE D1412 TRP 0.004 0.001 TRP A 128 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7260) covalent geometry : angle 0.57756 (10171) hydrogen bonds : bond 0.03866 ( 328) hydrogen bonds : angle 4.26000 ( 955) metal coordination : bond 0.00462 ( 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 94 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.211 Fit side-chains REVERT: A 5 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7781 (tp) REVERT: A 17 LYS cc_start: 0.8274 (ttpp) cc_final: 0.8026 (ttpp) REVERT: A 19 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8167 (mmtm) REVERT: A 300 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 436 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7795 (tt) REVERT: A 634 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6926 (tm-30) outliers start: 26 outliers final: 17 residues processed: 85 average time/residue: 0.4500 time to fit residues: 40.6523 Evaluate side-chains 87 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 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 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 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: 0.0370 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110185 restraints weight = 11006.489| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.49 r_work: 0.3308 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7263 Z= 0.178 Angle : 0.610 7.824 10171 Z= 0.329 Chirality : 0.041 0.128 1210 Planarity : 0.005 0.046 1104 Dihedral : 24.234 156.628 1523 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -0.51 (0.30), residues: 768 helix: 0.76 (0.23), residues: 514 sheet: 1.49 (1.48), residues: 12 loop : -2.92 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.008 0.001 TYR D1316 PHE 0.009 0.001 PHE D1412 TRP 0.004 0.001 TRP A 128 HIS 0.005 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7260) covalent geometry : angle 0.61015 (10171) hydrogen bonds : bond 0.04315 ( 328) hydrogen bonds : angle 4.32804 ( 955) metal coordination : bond 0.00593 ( 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 90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.215 Fit side-chains REVERT: A 5 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7796 (tp) REVERT: A 6 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7810 (mmm160) REVERT: A 17 LYS cc_start: 0.8303 (ttpp) cc_final: 0.8050 (ttpp) REVERT: A 19 LYS cc_start: 0.8451 (mmmm) cc_final: 0.8170 (mmtm) REVERT: A 436 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7859 (tt) REVERT: A 634 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6941 (tm-30) outliers start: 22 outliers final: 18 residues processed: 83 average time/residue: 0.4602 time to fit residues: 40.4922 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 : 0.219 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 75 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.0270 chunk 62 optimal weight: 0.0370 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111753 restraints weight = 11048.601| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.49 r_work: 0.3334 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7263 Z= 0.141 Angle : 0.584 9.089 10171 Z= 0.313 Chirality : 0.039 0.130 1210 Planarity : 0.005 0.046 1104 Dihedral : 24.213 157.619 1523 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.49 % Allowed : 18.14 % Favored : 78.37 % 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: -0.33 (0.30), residues: 768 helix: 0.89 (0.23), residues: 512 sheet: 1.71 (1.55), residues: 12 loop : -2.82 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1355 TYR 0.007 0.001 TYR D1316 PHE 0.004 0.001 PHE D1375 TRP 0.006 0.001 TRP A 128 HIS 0.005 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7260) covalent geometry : angle 0.58416 (10171) hydrogen bonds : bond 0.03602 ( 328) hydrogen bonds : angle 4.22911 ( 955) metal coordination : bond 0.00376 ( 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 91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.195 Fit side-chains REVERT: A 5 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7810 (tp) REVERT: A 6 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7855 (mmm160) REVERT: A 17 LYS cc_start: 0.8288 (ttpp) cc_final: 0.8027 (ttpp) REVERT: A 19 LYS cc_start: 0.8414 (mmmm) cc_final: 0.8141 (mmtm) REVERT: A 61 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7262 (mm-40) REVERT: A 300 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8003 (tp) REVERT: A 436 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7819 (tt) REVERT: A 634 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6913 (tm-30) outliers start: 21 outliers final: 17 residues processed: 83 average time/residue: 0.5015 time to fit residues: 43.8740 Evaluate side-chains 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110133 restraints weight = 10983.128| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.59 r_work: 0.3301 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7263 Z= 0.169 Angle : 0.604 9.252 10171 Z= 0.324 Chirality : 0.040 0.134 1210 Planarity : 0.005 0.046 1104 Dihedral : 24.234 156.948 1523 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.16 % Allowed : 18.64 % 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: -0.46 (0.30), residues: 768 helix: 0.80 (0.23), residues: 514 sheet: 1.84 (1.55), residues: 12 loop : -2.93 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1355 TYR 0.009 0.001 TYR D1316 PHE 0.004 0.001 PHE D1375 TRP 0.005 0.001 TRP A 128 HIS 0.004 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7260) covalent geometry : angle 0.60413 (10171) hydrogen bonds : bond 0.04143 ( 328) hydrogen bonds : angle 4.30177 ( 955) metal coordination : bond 0.00530 ( 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 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.240 Fit side-chains REVERT: A 5 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7773 (tp) REVERT: A 6 ARG cc_start: 0.8229 (mmm160) cc_final: 0.7840 (mmm160) REVERT: A 17 LYS cc_start: 0.8294 (ttpp) cc_final: 0.8036 (ttpp) REVERT: A 19 LYS cc_start: 0.8450 (mmmm) cc_final: 0.8174 (mmtm) REVERT: A 61 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7290 (mm-40) REVERT: A 436 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7783 (tt) REVERT: A 634 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7020 (tm-30) outliers start: 19 outliers final: 18 residues processed: 81 average time/residue: 0.5287 time to fit residues: 45.1714 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 : 0.140 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 64 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 55 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111811 restraints weight = 10933.098| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.50 r_work: 0.3329 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7263 Z= 0.141 Angle : 0.589 10.170 10171 Z= 0.315 Chirality : 0.039 0.132 1210 Planarity : 0.005 0.046 1104 Dihedral : 24.206 157.789 1523 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.00 % Allowed : 18.97 % Favored : 78.04 % 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: -0.31 (0.30), residues: 768 helix: 0.92 (0.23), residues: 512 sheet: 1.66 (1.57), residues: 12 loop : -2.83 (0.36), 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 0.004 0.001 PHE D1375 TRP 0.005 0.001 TRP A 128 HIS 0.005 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7260) covalent geometry : angle 0.58857 (10171) hydrogen bonds : bond 0.03568 ( 328) hydrogen bonds : angle 4.23376 ( 955) metal coordination : bond 0.00328 ( 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 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.158 Fit side-chains REVERT: A 5 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7777 (tp) REVERT: A 6 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7827 (mmm160) REVERT: A 17 LYS cc_start: 0.8269 (ttpp) cc_final: 0.8004 (ttpp) REVERT: A 19 LYS cc_start: 0.8410 (mmmm) cc_final: 0.8134 (mmtm) REVERT: A 61 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7266 (mm-40) REVERT: A 300 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7961 (tp) REVERT: A 436 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7737 (tt) REVERT: A 634 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6994 (tm-30) outliers start: 18 outliers final: 16 residues processed: 80 average time/residue: 0.5604 time to fit residues: 47.2271 Evaluate side-chains 87 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 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 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 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: 0.8980 chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 58 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109110 restraints weight = 10881.715| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.59 r_work: 0.3283 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7263 Z= 0.198 Angle : 0.637 9.558 10171 Z= 0.342 Chirality : 0.042 0.137 1210 Planarity : 0.005 0.046 1104 Dihedral : 24.251 156.578 1523 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.16 % Allowed : 18.97 % Favored : 77.87 % 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: -0.52 (0.30), residues: 768 helix: 0.76 (0.23), residues: 514 sheet: 1.84 (1.59), residues: 12 loop : -2.99 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1355 TYR 0.010 0.001 TYR D1316 PHE 0.006 0.001 PHE D1412 TRP 0.004 0.001 TRP A 128 HIS 0.007 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 7260) covalent geometry : angle 0.63695 (10171) hydrogen bonds : bond 0.04586 ( 328) hydrogen bonds : angle 4.36941 ( 955) metal coordination : bond 0.00628 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.70 seconds wall clock time: 34 minutes 2.12 seconds (2042.12 seconds total)