Starting phenix.real_space_refine on Fri Sep 11 00:05:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hhm_34804/09_2026/8hhm_34804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhm_34804/09_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_34804/09_2026/8hhm_34804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhm_34804/09_2026/8hhm_34804.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hhm_34804/09_2026/8hhm_34804.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hhm_34804/09_2026/8hhm_34804.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhm_34804/09_2026/8hhm_34804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhm_34804/09_2026/8hhm_34804.map" } 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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 1.36, per 1000 atoms: 0.24 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: 0.58 Conformation dependent library (CDL) restraints added in 333.0 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: 0.52 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: 1.03 Time building geometry restraints manager: 0.76 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: 7684 1.21 - 2.42: 396 2.42 - 3.64: 133 3.64 - 4.85: 16 4.85 - 6.06: 5 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: 2633 15.76 - 31.52: 360 31.52 - 47.28: 190 47.28 - 63.03: 102 63.03 - 78.79: 12 Dihedral angle restraints: 3297 sinusoidal: 1805 harmonic: 1492 Sorted by residual: dihedral pdb=" C4' G B -11 " pdb=" C3' G B -11 " pdb=" C2' G B -11 " pdb=" C1' G B -11 " ideal model delta sinusoidal sigma weight residual 36.35 -36.45 72.79 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' G C 101 " pdb=" C3' G C 101 " pdb=" C2' G C 101 " pdb=" C1' G C 101 " ideal model delta sinusoidal sigma weight residual 36.34 -35.61 71.96 1 3.10e+00 1.04e-01 6.90e+02 dihedral pdb=" C4' G B -8 " pdb=" C3' G B -8 " pdb=" C2' G B -8 " pdb=" C1' G B -8 " ideal model delta sinusoidal sigma weight residual 36.34 -35.56 71.90 1 3.10e+00 1.04e-01 6.89e+02 ... (remaining 3294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 768 0.058 - 0.115: 123 0.115 - 0.173: 7 0.173 - 0.230: 28 0.230 - 0.288: 25 Chirality restraints: 951 Sorted by residual: chirality pdb=" C2' G B -8 " pdb=" C3' G B -8 " pdb=" O2' G B -8 " pdb=" C1' G B -8 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' C B -12 " pdb=" C3' C B -12 " pdb=" O2' C B -12 " pdb=" C1' C B -12 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" P G B -7 " pdb=" OP1 G B -7 " pdb=" OP2 G B -7 " pdb=" O5' G B -7 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (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: 0.080 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: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.920 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.200 ------------------------------------------------------------------------------- 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= 0.330 Angle : 0.958 52.421 8237 Z= 0.468 Chirality : 0.067 0.288 951 Planarity : 0.005 0.030 803 Dihedral : 19.647 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 0.00515 / 0.33 ( 5821) covalent geometry : angle 0.69242 / 0.44 ( 8234) hydrogen bonds : bond 0.14709 / 7.58 ( 320) hydrogen bonds : angle 6.23753 / 2.64 ( 861) metal coordination : bond 0.02793 / 1.40 ( 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 : 0.122 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: 0.1126 time to fit residues: 13.9323 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 : 0.173 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.142989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.107832 restraints weight = 11091.765| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.57 r_work: 0.3542 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5825 Z= 0.238 Angle : 0.917 16.138 8237 Z= 0.421 Chirality : 0.070 0.708 951 Planarity : 0.005 0.051 803 Dihedral : 20.029 128.226 1404 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.82 % Allowed : 14.80 % Favored : 81.38 % 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: 1.23 (0.65), residues: 69 loop : -0.45 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 512 TYR 0.021 0.002 TYR A 576 PHE 0.011 0.001 PHE A 582 TRP 0.011 0.001 TRP A 440 HIS 0.003 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 ( 5821) covalent geometry : angle 0.89987 / 0.42 ( 8234) hydrogen bonds : bond 0.05701 / 2.92 ( 320) hydrogen bonds : angle 4.52979 / 1.85 ( 861) metal coordination : bond 0.02045 / 1.02 ( 4) metal coordination : angle 9.34587 / 3.12 ( 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 : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8085 (mmt) cc_final: 0.7861 (mpp) REVERT: A 340 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8820 (mm) REVERT: A 394 LEU cc_start: 0.8549 (tp) cc_final: 0.8135 (pp) REVERT: A 415 TRP cc_start: 0.7179 (m-10) cc_final: 0.6917 (m-10) REVERT: A 563 LEU cc_start: 0.8489 (mt) cc_final: 0.8224 (mm) outliers start: 16 outliers final: 10 residues processed: 79 average time/residue: 0.0995 time to fit residues: 9.7058 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 : 0.132 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 49 optimal weight: 0.3980 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 overall best weight: 3.4384 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.143957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.109285 restraints weight = 10935.834| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.51 r_work: 0.3563 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5825 Z= 0.183 Angle : 0.757 9.861 8237 Z= 0.361 Chirality : 0.059 0.586 951 Planarity : 0.005 0.030 803 Dihedral : 20.249 144.008 1402 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.10 % Allowed : 17.18 % Favored : 79.71 % 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: 1.86 (0.38), residues: 510 helix: 2.42 (0.33), residues: 260 sheet: 1.49 (0.63), residues: 69 loop : -0.69 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 547 TYR 0.020 0.002 TYR A 576 PHE 0.013 0.001 PHE A 582 TRP 0.011 0.001 TRP A 440 HIS 0.009 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 ( 5821) covalent geometry : angle 0.74325 / 0.36 ( 8234) hydrogen bonds : bond 0.05022 / 2.56 ( 320) hydrogen bonds : angle 4.18125 / 1.70 ( 861) metal coordination : bond 0.02065 / 1.03 ( 4) metal coordination : angle 7.68845 / 2.56 ( 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 67 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8003 (mmt) cc_final: 0.7783 (mpp) REVERT: A 177 LYS cc_start: 0.8035 (mmmm) cc_final: 0.7780 (tptp) REVERT: A 340 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8817 (mm) REVERT: A 394 LEU cc_start: 0.8561 (tp) cc_final: 0.8189 (pp) REVERT: A 415 TRP cc_start: 0.7008 (m-10) cc_final: 0.6773 (m-10) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.1077 time to fit residues: 8.3415 Evaluate side-chains 53 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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 350 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 581 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 40.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.144288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.109444 restraints weight = 10991.703| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.52 r_work: 0.3600 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5825 Z= 0.168 Angle : 0.731 9.646 8237 Z= 0.347 Chirality : 0.057 0.562 951 Planarity : 0.004 0.030 803 Dihedral : 20.114 140.636 1401 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.30 % Allowed : 16.95 % 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: 1.92 (0.38), residues: 510 helix: 2.48 (0.33), residues: 260 sheet: 1.50 (0.63), residues: 69 loop : -0.67 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 512 TYR 0.021 0.002 TYR A 576 PHE 0.006 0.001 PHE A 582 TRP 0.012 0.001 TRP A 442 HIS 0.006 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 ( 5821) covalent geometry : angle 0.71763 / 0.34 ( 8234) hydrogen bonds : bond 0.04815 / 2.45 ( 320) hydrogen bonds : angle 3.91318 / 1.58 ( 861) metal coordination : bond 0.01764 / 0.88 ( 4) metal coordination : angle 7.41064 / 2.47 ( 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 68 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8022 (mmt) cc_final: 0.7811 (mpp) REVERT: A 45 ASP cc_start: 0.8398 (t0) cc_final: 0.8188 (t0) REVERT: A 46 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 340 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8788 (mm) REVERT: A 394 LEU cc_start: 0.8525 (tp) cc_final: 0.8198 (pp) REVERT: A 415 TRP cc_start: 0.6947 (m-10) cc_final: 0.6678 (m-10) outliers start: 18 outliers final: 12 residues processed: 66 average time/residue: 0.0975 time to fit residues: 7.8985 Evaluate side-chains 58 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 5 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.142964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.108124 restraints weight = 11269.480| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.55 r_work: 0.3556 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5825 Z= 0.192 Angle : 0.734 9.908 8237 Z= 0.347 Chirality : 0.057 0.551 951 Planarity : 0.004 0.043 803 Dihedral : 20.100 141.308 1401 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.77 % Allowed : 17.90 % 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: 1.91 (0.38), residues: 510 helix: 2.49 (0.33), residues: 260 sheet: 1.63 (0.64), residues: 67 loop : -0.76 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 126 TYR 0.020 0.002 TYR A 576 PHE 0.005 0.001 PHE A 342 TRP 0.012 0.001 TRP A 442 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 ( 5821) covalent geometry : angle 0.72132 / 0.35 ( 8234) hydrogen bonds : bond 0.04872 / 2.48 ( 320) hydrogen bonds : angle 3.83631 / 1.54 ( 861) metal coordination : bond 0.01856 / 0.93 ( 4) metal coordination : angle 7.06248 / 2.35 ( 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 69 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8050 (mmt) cc_final: 0.7818 (mpp) REVERT: A 45 ASP cc_start: 0.8397 (t0) cc_final: 0.8184 (t0) REVERT: A 46 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7423 (mm) REVERT: A 340 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 365 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7774 (mm) REVERT: A 394 LEU cc_start: 0.8566 (tp) cc_final: 0.8236 (pp) REVERT: A 415 TRP cc_start: 0.7013 (m-10) cc_final: 0.6604 (m-10) outliers start: 20 outliers final: 13 residues processed: 63 average time/residue: 0.0891 time to fit residues: 7.1524 Evaluate side-chains 57 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 250 MET Chi-restraints excluded: chain A residue 272 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 50.0000 chunk 53 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.142212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107200 restraints weight = 11094.129| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.55 r_work: 0.3559 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5825 Z= 0.232 Angle : 0.758 10.461 8237 Z= 0.359 Chirality : 0.057 0.552 951 Planarity : 0.005 0.035 803 Dihedral : 20.172 140.314 1400 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.01 % Allowed : 17.90 % Favored : 77.09 % 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: 2.43 (0.33), residues: 261 sheet: 1.53 (0.64), residues: 67 loop : -0.77 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 458 TYR 0.019 0.002 TYR A 576 PHE 0.008 0.001 PHE A 421 TRP 0.011 0.001 TRP A 450 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 ( 5821) covalent geometry : angle 0.74820 / 0.36 ( 8234) hydrogen bonds : bond 0.05063 / 2.57 ( 320) hydrogen bonds : angle 3.89220 / 1.56 ( 861) metal coordination : bond 0.02067 / 1.03 ( 4) metal coordination : angle 6.51913 / 2.17 ( 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 70 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8078 (mmt) cc_final: 0.7872 (mpp) REVERT: A 45 ASP cc_start: 0.8429 (t0) cc_final: 0.8222 (t0) REVERT: A 46 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7590 (mm) REVERT: A 340 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 365 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 394 LEU cc_start: 0.8517 (tp) cc_final: 0.8179 (pp) REVERT: A 415 TRP cc_start: 0.7062 (m-10) cc_final: 0.6631 (m-10) REVERT: A 563 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8211 (mm) outliers start: 21 outliers final: 16 residues processed: 66 average time/residue: 0.0874 time to fit residues: 7.4059 Evaluate side-chains 62 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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 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 563 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 6 optimal weight: 40.0000 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 17 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 0.0570 overall best weight: 3.8106 ------------------------------------------------------------------------------- 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 = 0.138771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104989 restraints weight = 11140.730| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.46 r_work: 0.3469 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2785 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= 0.187 Angle : 0.723 9.749 8237 Z= 0.344 Chirality : 0.056 0.520 951 Planarity : 0.004 0.029 803 Dihedral : 20.180 140.711 1400 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 5.49 % Allowed : 17.66 % 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: 1.91 (0.38), residues: 510 helix: 2.44 (0.33), residues: 260 sheet: 1.55 (0.64), residues: 67 loop : -0.63 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 512 TYR 0.019 0.002 TYR A 576 PHE 0.010 0.001 PHE A 582 TRP 0.013 0.001 TRP A 442 HIS 0.010 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 ( 5821) covalent geometry : angle 0.71251 / 0.34 ( 8234) hydrogen bonds : bond 0.04833 / 2.47 ( 320) hydrogen bonds : angle 3.78316 / 1.52 ( 861) metal coordination : bond 0.02070 / 1.04 ( 4) metal coordination : angle 6.55199 / 2.18 ( 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 66 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8434 (t0) cc_final: 0.8206 (t0) REVERT: A 46 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7561 (mm) REVERT: A 127 LYS cc_start: 0.9183 (ttpp) cc_final: 0.8841 (tppt) REVERT: A 340 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8874 (mm) REVERT: A 365 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7739 (mm) REVERT: A 394 LEU cc_start: 0.8516 (tp) cc_final: 0.8188 (pp) REVERT: A 415 TRP cc_start: 0.7044 (m-10) cc_final: 0.6629 (m-10) outliers start: 23 outliers final: 15 residues processed: 62 average time/residue: 0.0807 time to fit residues: 6.5552 Evaluate side-chains 58 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 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 308 VAL 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: 9.9990 chunk 32 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 54 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.136964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102229 restraints weight = 11025.291| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.56 r_work: 0.3381 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2875 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= 0.212 Angle : 0.739 10.189 8237 Z= 0.351 Chirality : 0.056 0.532 951 Planarity : 0.004 0.031 803 Dihedral : 20.144 140.729 1400 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.53 % Allowed : 18.14 % 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: 1.86 (0.38), residues: 510 helix: 2.37 (0.33), residues: 260 sheet: 1.58 (0.64), residues: 67 loop : -0.60 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 512 TYR 0.019 0.002 TYR A 576 PHE 0.008 0.001 PHE A 582 TRP 0.011 0.001 TRP A 442 HIS 0.008 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 ( 5821) covalent geometry : angle 0.72916 / 0.35 ( 8234) hydrogen bonds : bond 0.04935 / 2.52 ( 320) hydrogen bonds : angle 3.83150 / 1.54 ( 861) metal coordination : bond 0.02035 / 1.02 ( 4) metal coordination : angle 6.22504 / 2.08 ( 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 63 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8547 (t0) cc_final: 0.8280 (t0) REVERT: A 46 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7491 (mm) REVERT: A 125 ARG cc_start: 0.8732 (mtt180) cc_final: 0.8383 (mtm180) REVERT: A 127 LYS cc_start: 0.9228 (ttpp) cc_final: 0.8857 (tppt) REVERT: A 340 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8790 (mm) REVERT: A 365 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7716 (mm) REVERT: A 394 LEU cc_start: 0.8491 (tp) cc_final: 0.8161 (pp) outliers start: 19 outliers final: 16 residues processed: 61 average time/residue: 0.0880 time to fit residues: 6.7787 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 : 0.165 ------------------------------------------------------------------------------- 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 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 308 VAL 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 474 VAL Chi-restraints excluded: chain A residue 581 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: 8.9990 chunk 55 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.136966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102611 restraints weight = 11027.675| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.51 r_work: 0.3384 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5825 Z= 0.217 Angle : 0.744 9.976 8237 Z= 0.355 Chirality : 0.056 0.536 951 Planarity : 0.005 0.030 803 Dihedral : 20.147 142.254 1400 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.77 % Allowed : 17.42 % Favored : 77.80 % 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: 1.90 (0.38), residues: 510 helix: 2.38 (0.33), residues: 260 sheet: 1.61 (0.64), residues: 67 loop : -0.57 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 512 TYR 0.019 0.002 TYR A 576 PHE 0.010 0.001 PHE A 582 TRP 0.051 0.002 TRP A 320 HIS 0.009 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 ( 5821) covalent geometry : angle 0.73490 / 0.35 ( 8234) hydrogen bonds : bond 0.04935 / 2.52 ( 320) hydrogen bonds : angle 3.77099 / 1.52 ( 861) metal coordination : bond 0.02131 / 1.07 ( 4) metal coordination : angle 6.17120 / 2.06 ( 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 64 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8543 (t0) cc_final: 0.8272 (t0) REVERT: A 46 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7513 (mm) REVERT: A 125 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8343 (mtm180) REVERT: A 127 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8862 (tppt) REVERT: A 365 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7727 (mm) REVERT: A 394 LEU cc_start: 0.8487 (tp) cc_final: 0.8168 (pp) outliers start: 20 outliers final: 16 residues processed: 61 average time/residue: 0.0831 time to fit residues: 6.4704 Evaluate side-chains 61 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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 308 VAL Chi-restraints excluded: chain A residue 329 VAL 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 474 VAL 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: 1.9990 chunk 10 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 overall best weight: 3.2126 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.138339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.103788 restraints weight = 11166.228| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.58 r_work: 0.3405 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3098 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= 0.165 Angle : 0.708 9.097 8237 Z= 0.337 Chirality : 0.055 0.526 951 Planarity : 0.004 0.030 803 Dihedral : 20.108 142.830 1398 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.06 % Allowed : 18.38 % Favored : 77.57 % 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: 2.06 (0.38), residues: 510 helix: 2.51 (0.33), residues: 260 sheet: 1.63 (0.64), residues: 67 loop : -0.46 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 512 TYR 0.021 0.002 TYR A 576 PHE 0.008 0.001 PHE A 582 TRP 0.028 0.002 TRP A 320 HIS 0.008 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 5821) covalent geometry : angle 0.69893 / 0.34 ( 8234) hydrogen bonds : bond 0.04633 / 2.36 ( 320) hydrogen bonds : angle 3.64451 / 1.46 ( 861) metal coordination : bond 0.02040 / 1.02 ( 4) metal coordination : angle 6.03472 / 2.01 ( 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 62 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8543 (t0) cc_final: 0.8263 (t0) REVERT: A 46 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7540 (mm) REVERT: A 125 ARG cc_start: 0.8691 (mtt180) cc_final: 0.8329 (mtm180) REVERT: A 127 LYS cc_start: 0.9186 (ttpp) cc_final: 0.8852 (tppt) REVERT: A 394 LEU cc_start: 0.8446 (tp) cc_final: 0.8139 (pp) REVERT: A 402 TYR cc_start: 0.5907 (t80) cc_final: 0.5695 (t80) REVERT: A 563 LEU cc_start: 0.8338 (mm) cc_final: 0.8061 (mm) REVERT: A 587 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6919 (mt) outliers start: 17 outliers final: 13 residues processed: 59 average time/residue: 0.0820 time to fit residues: 6.1645 Evaluate side-chains 59 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 210 LEU 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 329 VAL 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 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: 10.0000 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.137412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.102693 restraints weight = 11087.234| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.57 r_work: 0.3389 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5825 Z= 0.204 Angle : 0.740 9.744 8237 Z= 0.353 Chirality : 0.056 0.528 951 Planarity : 0.005 0.033 803 Dihedral : 20.110 144.471 1398 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.82 % Allowed : 18.62 % Favored : 77.57 % 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: 2.41 (0.33), residues: 260 sheet: 1.59 (0.63), residues: 67 loop : -0.47 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 512 TYR 0.033 0.002 TYR A 576 PHE 0.008 0.001 PHE A 582 TRP 0.079 0.002 TRP A 320 HIS 0.009 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 5821) covalent geometry : angle 0.73139 / 0.35 ( 8234) hydrogen bonds : bond 0.04804 / 2.44 ( 320) hydrogen bonds : angle 3.68666 / 1.48 ( 861) metal coordination : bond 0.01962 / 0.98 ( 4) metal coordination : angle 6.08993 / 2.03 ( 3) =============================================================================== Job complete usr+sys time: 1260.99 seconds wall clock time: 22 minutes 18.18 seconds (1338.18 seconds total)