Starting phenix.real_space_refine on Thu Jul 2 02:19:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hhm_34804/07_2026/8hhm_34804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhm_34804/07_2026/8hhm_34804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hhm_34804/07_2026/8hhm_34804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhm_34804/07_2026/8hhm_34804.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhm_34804/07_2026/8hhm_34804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhm_34804/07_2026/8hhm_34804.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hhm_34804/07_2026/8hhm_34804.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hhm_34804/07_2026/8hhm_34804.cif" } resolution = 3.08 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 ------------------------------------------------------------------------------- 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= -0.010 sd= 0.185 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 72 5.49 5 Mg 1 5.21 5 S 18 5.16 5 C 3200 2.51 5 N 1049 2.21 5 O 1217 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: 5558 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 871 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 23, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 34} Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 420 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4036 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p_pur': 1} Chain: "A" 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 5229 SG CYS A 552 87.653 21.706 13.199 1.00189.35 S ATOM 5362 SG CYS A 569 85.401 19.773 12.366 1.00191.57 S ATOM 5380 SG CYS A 572 87.817 17.121 13.902 1.00192.17 S Time building chain proxies: 1.11, per 1000 atoms: 0.20 Number of scatterers: 5558 At special positions: 0 Unit cell: (99.932, 84.826, 80.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 18 16.00 P 72 15.00 Mg 1 11.99 O 1217 8.00 N 1049 7.00 C 3200 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: 0.48 Conformation dependent library (CDL) restraints added in 274.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 569 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 572 " Number of angles added : 3 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 4 sheets defined 50.8% alpha, 16.3% beta 31 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 18 through 51 Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 176 Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.549A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.802A pdb=" N GLN A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 363 through 397 Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.117A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 479 removed outlier: 3.770A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 508 through 518 removed outlier: 3.895A pdb=" N ARG A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.593A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.187A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.714A pdb=" N ILE A 278 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG A 301 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 280 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 removed outlier: 6.570A pdb=" N ILE A 359 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR A 331 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY A 357 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.950A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 482 " --> pdb=" O THR A 538 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL A 540 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 484 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568 242 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.57 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: 1314 1.33 - 1.45: 1544 1.45 - 1.57: 2794 1.57 - 1.69: 140 1.69 - 1.81: 29 Bond restraints: 5821 Sorted by residual: bond pdb=" C1' DT C 10 " pdb=" N1 DT C 10 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.53e+00 bond pdb=" C1' DC C 9 " pdb=" N1 DC C 9 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.26e+00 bond pdb=" C3' DT D 26 " pdb=" O3' DT D 26 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.19e+00 bond pdb=" C1' DC C 8 " pdb=" N1 DC C 8 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.88e+00 bond pdb=" C3' DA C 19 " pdb=" O3' DA C 19 " ideal model delta sigma weight residual 1.435 1.403 0.032 1.30e-02 5.92e+03 5.88e+00 ... (remaining 5816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7821 1.21 - 2.42: 345 2.42 - 3.64: 61 3.64 - 4.85: 5 4.85 - 6.06: 2 Bond angle restraints: 8234 Sorted by residual: angle pdb=" N3 DT C 10 " pdb=" C4 DT C 10 " pdb=" O4 DT C 10 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT D 24 " pdb=" C4 DT D 24 " pdb=" O4 DT D 24 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT D 28 " pdb=" C4 DT D 28 " pdb=" O4 DT D 28 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT C 15 " pdb=" C4 DT C 15 " pdb=" O4 DT C 15 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT C 13 " pdb=" C4 DT C 13 " pdb=" O4 DT C 13 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 ... (remaining 8229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 2702 15.76 - 31.52: 344 31.52 - 47.28: 167 47.28 - 63.03: 77 63.03 - 78.79: 7 Dihedral angle restraints: 3297 sinusoidal: 1805 harmonic: 1492 Sorted by residual: dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -168.18 62.18 1 1.70e+01 3.46e-03 1.77e+01 dihedral pdb=" CG ARG A 513 " pdb=" CD ARG A 513 " pdb=" NE ARG A 513 " pdb=" CZ ARG A 513 " ideal model delta sinusoidal sigma weight residual 180.00 136.03 43.97 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA ASP A 477 " pdb=" CB ASP A 477 " pdb=" CG ASP A 477 " pdb=" OD1 ASP A 477 " ideal model delta sinusoidal sigma weight residual -30.00 -84.88 54.88 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 3294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 544 0.026 - 0.052: 245 0.052 - 0.077: 97 0.077 - 0.103: 42 0.103 - 0.129: 23 Chirality restraints: 951 Sorted by residual: chirality pdb=" C3' DC C 16 " pdb=" C4' DC C 16 " pdb=" O3' DC C 16 " pdb=" C2' DC C 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE A 359 " pdb=" N ILE A 359 " pdb=" C ILE A 359 " pdb=" CB ILE A 359 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL A 361 " pdb=" N VAL A 361 " pdb=" C VAL A 361 " pdb=" CB VAL A 361 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 948 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C GLN A 452 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A 452 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 453 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 468 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C TYR A 468 " 0.029 2.00e-02 2.50e+03 pdb=" O TYR A 468 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 469 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 462 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C GLY A 462 " 0.027 2.00e-02 2.50e+03 pdb=" O GLY A 462 " -0.010 2.00e-02 2.50e+03 pdb=" N HIS A 463 " -0.009 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 140 2.66 - 3.22: 5023 3.22 - 3.78: 9599 3.78 - 4.34: 12510 4.34 - 4.90: 19151 Nonbonded interactions: 46423 Sorted by model distance: nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 2.106 2.170 nonbonded pdb=" OG1 THR A 3 " pdb=" OD1 ASP A 304 " model vdw 2.210 3.040 nonbonded pdb=" O TRP A 428 " pdb=" OG SER A 436 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A 334 " pdb=" O ALA A 336 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR A 468 " pdb=" O ALA A 517 " model vdw 2.305 3.040 ... (remaining 46418 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: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.370 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 0.044 5825 Z= 0.328 Angle : 0.882 52.421 8237 Z= 0.448 Chirality : 0.039 0.129 951 Planarity : 0.005 0.030 803 Dihedral : 17.912 78.793 2329 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.34 % Allowed : 12.65 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.39), residues: 510 helix: 1.71 (0.34), residues: 252 sheet: 0.63 (0.63), residues: 81 loop : -0.24 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.009 0.001 TYR A 217 PHE 0.013 0.002 PHE A 582 TRP 0.010 0.001 TRP A 440 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.33 ( 5821) covalent geometry : angle 0.58365 / 0.42 ( 8234) hydrogen bonds : bond 0.14709 / 8.77 ( 320) hydrogen bonds : angle 6.23753 / 3.59 ( 861) metal coordination : bond 0.02793 / 1.74 ( 4) metal coordination : angle 34.67092 / 11.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.8183 (mmt) cc_final: 0.7952 (mpp) REVERT: A 19 GLU cc_start: 0.8336 (tp30) cc_final: 0.7901 (tp30) REVERT: A 46 LEU cc_start: 0.7829 (mt) cc_final: 0.7523 (mt) REVERT: A 127 LYS cc_start: 0.9246 (tppt) cc_final: 0.9007 (tppt) REVERT: A 327 THR cc_start: 0.8918 (m) cc_final: 0.8522 (m) REVERT: A 340 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8897 (mm) REVERT: A 370 THR cc_start: 0.8726 (m) cc_final: 0.8350 (p) REVERT: A 408 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8651 (mm-30) REVERT: A 563 LEU cc_start: 0.8523 (mt) cc_final: 0.8307 (mm) outliers start: 14 outliers final: 5 residues processed: 104 average time/residue: 0.1069 time to fit residues: 13.2488 Evaluate side-chains 65 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 50.0000 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 317 HIS A 374 ASN A 431 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.141340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107066 restraints weight = 11120.038| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.54 r_work: 0.3528 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5825 Z= 0.214 Angle : 0.617 12.836 8237 Z= 0.329 Chirality : 0.039 0.144 951 Planarity : 0.005 0.047 803 Dihedral : 18.043 80.380 1404 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.82 % Allowed : 15.04 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.38), residues: 510 helix: 2.23 (0.33), residues: 260 sheet: 1.21 (0.65), residues: 69 loop : -0.43 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 512 TYR 0.020 0.002 TYR A 576 PHE 0.011 0.001 PHE A 582 TRP 0.012 0.001 TRP A 440 HIS 0.002 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 ( 5821) covalent geometry : angle 0.59178 / 0.33 ( 8234) hydrogen bonds : bond 0.05580 / 3.23 ( 320) hydrogen bonds : angle 4.51669 / 2.56 ( 861) metal coordination : bond 0.01809 / 1.02 ( 4) metal coordination : angle 9.13052 / 3.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8133 (mmt) cc_final: 0.7911 (mpp) REVERT: A 340 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8823 (mm) REVERT: A 394 LEU cc_start: 0.8559 (tp) cc_final: 0.8150 (pp) REVERT: A 415 TRP cc_start: 0.7175 (m-10) cc_final: 0.6917 (m-10) REVERT: A 563 LEU cc_start: 0.8487 (mt) cc_final: 0.8224 (mm) outliers start: 16 outliers final: 10 residues processed: 79 average time/residue: 0.1005 time to fit residues: 9.7478 Evaluate side-chains 56 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 581 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 49 optimal weight: 0.0170 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.144692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109143 restraints weight = 10973.744| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.56 r_work: 0.3562 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5825 Z= 0.151 Angle : 0.556 9.875 8237 Z= 0.297 Chirality : 0.037 0.133 951 Planarity : 0.004 0.043 803 Dihedral : 17.974 79.991 1402 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.15 % Allowed : 17.90 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.38), residues: 510 helix: 2.45 (0.33), residues: 260 sheet: 1.41 (0.63), residues: 69 loop : -0.51 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 513 TYR 0.020 0.002 TYR A 576 PHE 0.011 0.001 PHE A 582 TRP 0.010 0.001 TRP A 440 HIS 0.008 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 5821) covalent geometry : angle 0.53667 / 0.29 ( 8234) hydrogen bonds : bond 0.04854 / 2.83 ( 320) hydrogen bonds : angle 4.14231 / 2.36 ( 861) metal coordination : bond 0.02029 / 1.04 ( 4) metal coordination : angle 7.71988 / 2.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8039 (mmmm) cc_final: 0.7781 (tptp) REVERT: A 340 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8810 (mm) REVERT: A 394 LEU cc_start: 0.8549 (tp) cc_final: 0.8180 (pp) REVERT: A 415 TRP cc_start: 0.7022 (m-10) cc_final: 0.6750 (m-10) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 0.1094 time to fit residues: 8.3016 Evaluate side-chains 48 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.142315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.107759 restraints weight = 11035.935| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.53 r_work: 0.3565 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5825 Z= 0.171 Angle : 0.552 9.163 8237 Z= 0.294 Chirality : 0.037 0.173 951 Planarity : 0.004 0.031 803 Dihedral : 17.869 80.033 1401 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.01 % Allowed : 16.23 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.38), residues: 510 helix: 2.45 (0.33), residues: 260 sheet: 1.37 (0.64), residues: 69 loop : -0.52 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 513 TYR 0.020 0.002 TYR A 576 PHE 0.006 0.001 PHE A 582 TRP 0.010 0.001 TRP A 442 HIS 0.006 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 5821) covalent geometry : angle 0.53333 / 0.29 ( 8234) hydrogen bonds : bond 0.04828 / 2.82 ( 320) hydrogen bonds : angle 3.93947 / 2.22 ( 861) metal coordination : bond 0.01775 / 0.91 ( 4) metal coordination : angle 7.44836 / 2.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8474 (t0) cc_final: 0.8237 (t0) REVERT: A 46 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7530 (mm) REVERT: A 340 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8817 (mm) REVERT: A 394 LEU cc_start: 0.8527 (tp) cc_final: 0.8199 (pp) outliers start: 21 outliers final: 13 residues processed: 71 average time/residue: 0.1132 time to fit residues: 9.6924 Evaluate side-chains 58 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 581 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.142799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.108380 restraints weight = 11211.501| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.54 r_work: 0.3570 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5825 Z= 0.150 Angle : 0.535 8.543 8237 Z= 0.284 Chirality : 0.036 0.158 951 Planarity : 0.005 0.063 803 Dihedral : 17.822 79.669 1401 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.82 % Allowed : 18.85 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.38), residues: 510 helix: 2.54 (0.33), residues: 260 sheet: 1.66 (0.63), residues: 67 loop : -0.71 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 513 TYR 0.020 0.002 TYR A 576 PHE 0.005 0.001 PHE A 582 TRP 0.013 0.001 TRP A 415 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 ( 5821) covalent geometry : angle 0.51714 / 0.28 ( 8234) hydrogen bonds : bond 0.04574 / 2.68 ( 320) hydrogen bonds : angle 3.78540 / 2.11 ( 861) metal coordination : bond 0.01807 / 0.92 ( 4) metal coordination : angle 7.15366 / 2.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8429 (t0) cc_final: 0.8213 (t0) REVERT: A 46 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7442 (mm) REVERT: A 340 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8813 (mm) REVERT: A 394 LEU cc_start: 0.8524 (tp) cc_final: 0.8190 (pp) outliers start: 16 outliers final: 10 residues processed: 62 average time/residue: 0.0804 time to fit residues: 6.3926 Evaluate side-chains 55 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 581 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 4 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.140647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106300 restraints weight = 11082.789| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.52 r_work: 0.3483 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5825 Z= 0.238 Angle : 0.586 8.354 8237 Z= 0.310 Chirality : 0.039 0.124 951 Planarity : 0.005 0.044 803 Dihedral : 17.925 80.233 1399 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 5.01 % Allowed : 18.38 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.38), residues: 510 helix: 2.45 (0.33), residues: 260 sheet: 1.55 (0.64), residues: 67 loop : -0.80 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 513 TYR 0.019 0.002 TYR A 576 PHE 0.009 0.001 PHE A 582 TRP 0.012 0.002 TRP A 450 HIS 0.009 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 ( 5821) covalent geometry : angle 0.57234 / 0.31 ( 8234) hydrogen bonds : bond 0.05047 / 2.95 ( 320) hydrogen bonds : angle 3.90774 / 2.19 ( 861) metal coordination : bond 0.02068 / 1.05 ( 4) metal coordination : angle 6.70312 / 2.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8456 (t0) cc_final: 0.8234 (t0) REVERT: A 46 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7632 (mm) REVERT: A 340 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8856 (mm) REVERT: A 394 LEU cc_start: 0.8513 (tp) cc_final: 0.8190 (pp) outliers start: 21 outliers final: 15 residues processed: 64 average time/residue: 0.0721 time to fit residues: 5.9931 Evaluate side-chains 60 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 581 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.138854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105802 restraints weight = 11126.552| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.45 r_work: 0.3483 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5825 Z= 0.132 Angle : 0.523 8.197 8237 Z= 0.278 Chirality : 0.036 0.142 951 Planarity : 0.004 0.032 803 Dihedral : 17.850 79.422 1399 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 5.01 % Allowed : 18.62 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.04 (0.38), residues: 510 helix: 2.59 (0.33), residues: 260 sheet: 1.60 (0.64), residues: 67 loop : -0.62 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 513 TYR 0.021 0.002 TYR A 576 PHE 0.007 0.001 PHE A 582 TRP 0.014 0.001 TRP A 442 HIS 0.008 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 5821) covalent geometry : angle 0.50686 / 0.28 ( 8234) hydrogen bonds : bond 0.04435 / 2.60 ( 320) hydrogen bonds : angle 3.68061 / 2.05 ( 861) metal coordination : bond 0.01955 / 0.98 ( 4) metal coordination : angle 6.70376 / 2.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8448 (t0) cc_final: 0.8228 (t0) REVERT: A 46 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7592 (mm) REVERT: A 325 GLU cc_start: 0.7734 (mp0) cc_final: 0.7528 (pm20) REVERT: A 340 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8864 (mm) REVERT: A 394 LEU cc_start: 0.8481 (tp) cc_final: 0.8154 (pp) outliers start: 21 outliers final: 17 residues processed: 63 average time/residue: 0.0744 time to fit residues: 6.0113 Evaluate side-chains 62 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 34 optimal weight: 10.0000 chunk 43 optimal weight: 0.0270 chunk 54 optimal weight: 20.0000 overall best weight: 1.5042 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.140074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.107093 restraints weight = 11001.776| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.42 r_work: 0.3510 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5825 Z= 0.113 Angle : 0.504 7.887 8237 Z= 0.269 Chirality : 0.035 0.134 951 Planarity : 0.004 0.034 803 Dihedral : 17.663 79.117 1399 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.58 % Allowed : 19.57 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.20 (0.38), residues: 510 helix: 2.72 (0.33), residues: 260 sheet: 1.69 (0.64), residues: 67 loop : -0.56 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 512 TYR 0.021 0.001 TYR A 576 PHE 0.005 0.001 PHE A 155 TRP 0.016 0.001 TRP A 442 HIS 0.010 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 5821) covalent geometry : angle 0.48829 / 0.27 ( 8234) hydrogen bonds : bond 0.04128 / 2.43 ( 320) hydrogen bonds : angle 3.49401 / 1.96 ( 861) metal coordination : bond 0.01795 / 0.91 ( 4) metal coordination : angle 6.64154 / 2.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8426 (t0) cc_final: 0.8214 (t0) REVERT: A 46 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7525 (mm) REVERT: A 325 GLU cc_start: 0.7844 (mp0) cc_final: 0.7637 (pm20) REVERT: A 340 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 394 LEU cc_start: 0.8450 (tp) cc_final: 0.8135 (pp) REVERT: A 402 TYR cc_start: 0.6019 (t80) cc_final: 0.5244 (t80) outliers start: 15 outliers final: 8 residues processed: 56 average time/residue: 0.0830 time to fit residues: 5.8206 Evaluate side-chains 52 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.137516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.104017 restraints weight = 11063.873| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.45 r_work: 0.3456 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5825 Z= 0.222 Angle : 0.584 7.823 8237 Z= 0.309 Chirality : 0.038 0.163 951 Planarity : 0.005 0.036 803 Dihedral : 17.755 79.444 1398 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.58 % Allowed : 19.81 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.38), residues: 510 helix: 2.47 (0.33), residues: 260 sheet: 1.62 (0.64), residues: 67 loop : -0.64 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 512 TYR 0.018 0.002 TYR A 576 PHE 0.010 0.002 PHE A 582 TRP 0.049 0.002 TRP A 320 HIS 0.011 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 ( 5821) covalent geometry : angle 0.57169 / 0.31 ( 8234) hydrogen bonds : bond 0.04666 / 2.73 ( 320) hydrogen bonds : angle 3.66042 / 2.08 ( 861) metal coordination : bond 0.02025 / 1.03 ( 4) metal coordination : angle 6.31042 / 2.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8440 (t0) cc_final: 0.8209 (t0) REVERT: A 46 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7644 (mm) REVERT: A 125 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8392 (ptp-170) REVERT: A 127 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8835 (tppt) REVERT: A 325 GLU cc_start: 0.7888 (mp0) cc_final: 0.7667 (pm20) REVERT: A 340 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8894 (mm) REVERT: A 394 LEU cc_start: 0.8487 (tp) cc_final: 0.8167 (pp) outliers start: 15 outliers final: 12 residues processed: 60 average time/residue: 0.0834 time to fit residues: 6.2881 Evaluate side-chains 59 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.139047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105707 restraints weight = 11060.619| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.46 r_work: 0.3481 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5825 Z= 0.145 Angle : 0.542 7.928 8237 Z= 0.288 Chirality : 0.036 0.141 951 Planarity : 0.004 0.030 803 Dihedral : 17.755 79.024 1398 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.34 % Allowed : 20.29 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.38), residues: 510 helix: 2.51 (0.33), residues: 260 sheet: 1.60 (0.64), residues: 67 loop : -0.60 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 512 TYR 0.020 0.002 TYR A 576 PHE 0.008 0.001 PHE A 582 TRP 0.079 0.003 TRP A 320 HIS 0.011 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 5821) covalent geometry : angle 0.52855 / 0.29 ( 8234) hydrogen bonds : bond 0.04305 / 2.52 ( 320) hydrogen bonds : angle 3.56649 / 2.03 ( 861) metal coordination : bond 0.02024 / 1.02 ( 4) metal coordination : angle 6.33547 / 2.11 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8455 (t0) cc_final: 0.8223 (t0) REVERT: A 46 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7581 (mm) REVERT: A 125 ARG cc_start: 0.8688 (mtt180) cc_final: 0.8373 (ptp-170) REVERT: A 325 GLU cc_start: 0.7962 (mp0) cc_final: 0.7736 (pm20) REVERT: A 340 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8911 (mm) REVERT: A 394 LEU cc_start: 0.8474 (tp) cc_final: 0.8167 (pp) outliers start: 14 outliers final: 10 residues processed: 58 average time/residue: 0.0833 time to fit residues: 6.1085 Evaluate side-chains 57 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.138320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105007 restraints weight = 10974.004| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.45 r_work: 0.3468 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5825 Z= 0.170 Angle : 0.560 8.988 8237 Z= 0.296 Chirality : 0.037 0.131 951 Planarity : 0.004 0.028 803 Dihedral : 17.757 79.306 1398 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.86 % Allowed : 20.76 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.38), residues: 510 helix: 2.43 (0.33), residues: 260 sheet: 1.60 (0.64), residues: 67 loop : -0.59 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 512 TYR 0.019 0.002 TYR A 576 PHE 0.008 0.001 PHE A 582 TRP 0.037 0.002 TRP A 320 HIS 0.009 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 5821) covalent geometry : angle 0.54813 / 0.29 ( 8234) hydrogen bonds : bond 0.04453 / 2.61 ( 320) hydrogen bonds : angle 3.60982 / 2.06 ( 861) metal coordination : bond 0.02051 / 1.03 ( 4) metal coordination : angle 6.10124 / 2.03 ( 3) =============================================================================== Job complete usr+sys time: 1169.43 seconds wall clock time: 20 minutes 47.76 seconds (1247.76 seconds total)