Starting phenix.real_space_refine on Fri Aug 22 16:24:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhm_34804/08_2025/8hhm_34804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhm_34804/08_2025/8hhm_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_34804/08_2025/8hhm_34804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhm_34804/08_2025/8hhm_34804.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhm_34804/08_2025/8hhm_34804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhm_34804/08_2025/8hhm_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-2.0-5787/lib/python3.9/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: 1.48, per 1000 atoms: 0.27 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 223.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.71 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: 1.11 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=" N THR A 3 " pdb=" CA THR A 3 " ideal model delta sigma weight residual 1.466 1.452 0.015 1.36e-02 5.41e+03 1.21e+00 bond pdb=" CA HIS A 463 " pdb=" C HIS A 463 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.32e-02 5.74e+03 8.43e-01 bond pdb=" C MET A 9 " pdb=" N GLY A 10 " ideal model delta sigma weight residual 1.332 1.328 0.004 5.00e-03 4.00e+04 8.08e-01 bond pdb=" C3' DG D 23 " pdb=" O3' DG D 23 " ideal model delta sigma weight residual 1.422 1.448 -0.026 3.00e-02 1.11e+03 7.80e-01 bond pdb=" CG1 ILE A 278 " pdb=" CD1 ILE A 278 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 6.96e-01 ... (remaining 5816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7926 1.21 - 2.42: 265 2.42 - 3.64: 36 3.64 - 4.85: 5 4.85 - 6.06: 2 Bond angle restraints: 8234 Sorted by residual: angle pdb=" C VAL A 329 " pdb=" N ALA A 330 " pdb=" CA ALA A 330 " ideal model delta sigma weight residual 121.75 117.77 3.98 1.73e+00 3.34e-01 5.29e+00 angle pdb=" N VAL A 329 " pdb=" CA VAL A 329 " pdb=" C VAL A 329 " ideal model delta sigma weight residual 109.34 113.63 -4.29 2.08e+00 2.31e-01 4.25e+00 angle pdb=" CA VAL A 329 " pdb=" C VAL A 329 " pdb=" N ALA A 330 " ideal model delta sigma weight residual 116.60 119.57 -2.97 1.45e+00 4.76e-01 4.19e+00 angle pdb=" C1' G B -27 " pdb=" N9 G B -27 " pdb=" C4 G B -27 " ideal model delta sigma weight residual 126.50 132.56 -6.06 3.00e+00 1.11e-01 4.08e+00 angle pdb=" C GLN A 453 " pdb=" N GLU A 454 " pdb=" CA GLU A 454 " ideal model delta sigma weight residual 121.80 117.46 4.34 2.16e+00 2.14e-01 4.04e+00 ... (remaining 8229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 2753 15.76 - 31.52: 353 31.52 - 47.28: 200 47.28 - 63.03: 106 63.03 - 78.79: 45 Dihedral angle restraints: 3457 sinusoidal: 1965 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 3454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 567 0.026 - 0.052: 247 0.052 - 0.077: 90 0.077 - 0.103: 30 0.103 - 0.129: 17 Chirality restraints: 951 Sorted by residual: 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 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-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: 0.060 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.290 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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= 0.215 Angle : 0.850 52.421 8237 Z= 0.343 Chirality : 0.036 0.129 951 Planarity : 0.005 0.030 803 Dihedral : 20.700 78.793 2489 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 aren 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 covalent geometry : bond 0.00451 ( 5821) covalent geometry : angle 0.53400 ( 8234) hydrogen bonds : bond 0.14709 ( 320) hydrogen bonds : angle 6.23753 ( 861) metal coordination : bond 0.02793 ( 4) metal coordination : angle 34.67092 ( 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 : 0.147 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: 0.1233 time to fit residues: 15.1965 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 : 0.192 ------------------------------------------------------------------------------- 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: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4165 r_free = 0.4165 target = 0.142374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107106 restraints weight = 11111.653| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.60 r_work: 0.3529 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5825 Z= 0.211 Angle : 0.590 12.928 8237 Z= 0.309 Chirality : 0.037 0.136 951 Planarity : 0.005 0.037 803 Dihedral : 22.009 78.947 1564 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.82 % Allowed : 15.27 % Favored : 80.91 % 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 aren not related in a simple way. whole: 1.81 (0.39), residues: 510 helix: 2.32 (0.33), residues: 260 sheet: 1.36 (0.64), residues: 69 loop : -0.55 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 125 TYR 0.019 0.002 TYR A 576 PHE 0.010 0.002 PHE A 582 TRP 0.013 0.001 TRP A 440 HIS 0.003 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 5821) covalent geometry : angle 0.56389 ( 8234) hydrogen bonds : bond 0.05044 ( 320) hydrogen bonds : angle 4.34592 ( 861) metal coordination : bond 0.03060 ( 4) metal coordination : angle 9.10849 ( 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 : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8073 (mmt) cc_final: 0.7855 (mpp) REVERT: A 340 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8821 (mm) REVERT: A 394 LEU cc_start: 0.8571 (tp) cc_final: 0.8186 (pp) REVERT: A 415 TRP cc_start: 0.7152 (m-10) cc_final: 0.6858 (m-10) REVERT: A 563 LEU cc_start: 0.8501 (mt) cc_final: 0.8227 (mm) outliers start: 16 outliers final: 10 residues processed: 79 average time/residue: 0.1088 time to fit residues: 10.3767 Evaluate side-chains 55 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 49 optimal weight: 0.2980 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.143766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.108801 restraints weight = 11008.312| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.58 r_work: 0.3579 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5825 Z= 0.140 Angle : 0.533 10.006 8237 Z= 0.282 Chirality : 0.034 0.127 951 Planarity : 0.004 0.044 803 Dihedral : 21.860 78.177 1562 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.39 % Allowed : 17.66 % 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 aren not related in a simple way. whole: 2.01 (0.38), residues: 510 helix: 2.51 (0.33), residues: 260 sheet: 1.54 (0.64), residues: 69 loop : -0.56 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 513 TYR 0.019 0.002 TYR A 576 PHE 0.006 0.001 PHE A 582 TRP 0.012 0.001 TRP A 442 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5821) covalent geometry : angle 0.51059 ( 8234) hydrogen bonds : bond 0.04475 ( 320) hydrogen bonds : angle 3.90762 ( 861) metal coordination : bond 0.01283 ( 4) metal coordination : angle 8.06297 ( 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: 10 poor density : 55 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7835 (tptp) REVERT: A 340 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8812 (mm) REVERT: A 394 LEU cc_start: 0.8512 (tp) cc_final: 0.8189 (pp) REVERT: A 415 TRP cc_start: 0.6937 (m-10) cc_final: 0.6625 (m-10) REVERT: A 530 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8167 (mmp) outliers start: 10 outliers final: 3 residues processed: 61 average time/residue: 0.1032 time to fit residues: 7.7328 Evaluate side-chains 52 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 530 MET 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: 0.9980 chunk 51 optimal weight: 0.0060 chunk 33 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 0.0000 chunk 6 optimal weight: 10.0000 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.144102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.110271 restraints weight = 10953.181| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.52 r_work: 0.3587 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5825 Z= 0.121 Angle : 0.516 9.073 8237 Z= 0.271 Chirality : 0.034 0.142 951 Planarity : 0.004 0.033 803 Dihedral : 21.728 77.768 1558 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.10 % Allowed : 17.42 % Favored : 79.47 % 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 aren not related in a simple way. whole: 2.14 (0.38), residues: 510 helix: 2.61 (0.32), residues: 260 sheet: 1.53 (0.63), residues: 69 loop : -0.43 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 513 TYR 0.019 0.001 TYR A 576 PHE 0.003 0.001 PHE A 342 TRP 0.013 0.001 TRP A 442 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 5821) covalent geometry : angle 0.49431 ( 8234) hydrogen bonds : bond 0.04109 ( 320) hydrogen bonds : angle 3.66400 ( 861) metal coordination : bond 0.01056 ( 4) metal coordination : angle 7.74983 ( 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: 13 poor density : 60 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7796 (tptp) REVERT: A 340 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 394 LEU cc_start: 0.8526 (tp) cc_final: 0.8201 (pp) outliers start: 13 outliers final: 5 residues processed: 68 average time/residue: 0.1001 time to fit residues: 8.4959 Evaluate side-chains 56 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 340 ILE Chi-restraints excluded: chain A residue 350 VAL 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: 6.9990 chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.143113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108401 restraints weight = 11251.976| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.59 r_work: 0.3556 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5825 Z= 0.168 Angle : 0.537 8.659 8237 Z= 0.282 Chirality : 0.036 0.186 951 Planarity : 0.004 0.046 803 Dihedral : 21.703 78.006 1558 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.30 % Allowed : 17.42 % Favored : 78.28 % 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 aren not related in a simple way. whole: 2.07 (0.38), residues: 510 helix: 2.59 (0.33), residues: 260 sheet: 1.72 (0.64), residues: 67 loop : -0.62 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 513 TYR 0.019 0.002 TYR A 576 PHE 0.006 0.001 PHE A 421 TRP 0.011 0.001 TRP A 442 HIS 0.002 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5821) covalent geometry : angle 0.51872 ( 8234) hydrogen bonds : bond 0.04345 ( 320) hydrogen bonds : angle 3.69082 ( 861) metal coordination : bond 0.01480 ( 4) metal coordination : angle 7.37918 ( 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: 18 poor density : 51 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7543 (mm) REVERT: A 177 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7734 (tptp) REVERT: A 340 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8841 (mm) REVERT: A 394 LEU cc_start: 0.8537 (tp) cc_final: 0.8197 (pp) REVERT: A 530 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8163 (mmp) outliers start: 18 outliers final: 11 residues processed: 64 average time/residue: 0.0933 time to fit residues: 7.4593 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 : 0.104 ------------------------------------------------------------------------------- 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 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 360 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 50 optimal weight: 40.0000 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.136347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.103278 restraints weight = 10946.943| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.45 r_work: 0.3439 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2662 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= 0.244 Angle : 0.587 8.137 8237 Z= 0.310 Chirality : 0.039 0.132 951 Planarity : 0.005 0.042 803 Dihedral : 21.773 78.616 1558 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.30 % Allowed : 17.42 % Favored : 78.28 % 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 aren not related in a simple way. whole: 1.83 (0.38), residues: 510 helix: 2.38 (0.33), residues: 260 sheet: 1.60 (0.64), residues: 67 loop : -0.70 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 458 TYR 0.018 0.002 TYR A 576 PHE 0.008 0.002 PHE A 421 TRP 0.013 0.002 TRP A 450 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 5821) covalent geometry : angle 0.57289 ( 8234) hydrogen bonds : bond 0.04850 ( 320) hydrogen bonds : angle 3.84745 ( 861) metal coordination : bond 0.02125 ( 4) metal coordination : angle 6.61128 ( 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 66 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7649 (mm) REVERT: A 177 LYS cc_start: 0.8031 (mmmm) cc_final: 0.7688 (tptp) REVERT: A 340 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8881 (mm) REVERT: A 365 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7595 (mm) REVERT: A 394 LEU cc_start: 0.8517 (tp) cc_final: 0.8192 (pp) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 0.0975 time to fit residues: 7.7579 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 : 0.107 ------------------------------------------------------------------------------- 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 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 360 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 ILE 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: 9.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.136084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103046 restraints weight = 11135.146| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.43 r_work: 0.3434 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2791 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= 0.236 Angle : 0.582 7.359 8237 Z= 0.307 Chirality : 0.038 0.211 951 Planarity : 0.004 0.031 803 Dihedral : 21.815 78.736 1558 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.82 % Allowed : 17.18 % Favored : 79.00 % 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 aren not related in a simple way. whole: 1.72 (0.38), residues: 510 helix: 2.26 (0.33), residues: 262 sheet: 1.35 (0.65), residues: 69 loop : -0.66 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 458 TYR 0.019 0.002 TYR A 576 PHE 0.009 0.002 PHE A 582 TRP 0.012 0.002 TRP A 450 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 5821) covalent geometry : angle 0.57093 ( 8234) hydrogen bonds : bond 0.04783 ( 320) hydrogen bonds : angle 3.83490 ( 861) metal coordination : bond 0.02093 ( 4) metal coordination : angle 5.97454 ( 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: 16 poor density : 50 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 177 LYS cc_start: 0.7797 (mmmm) cc_final: 0.7554 (tptp) REVERT: A 340 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8891 (mm) REVERT: A 365 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 394 LEU cc_start: 0.8501 (tp) cc_final: 0.8182 (pp) outliers start: 16 outliers final: 10 residues processed: 64 average time/residue: 0.0973 time to fit residues: 7.8466 Evaluate side-chains 56 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 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 147 ASP 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 581 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 20 optimal weight: 0.0040 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 overall best weight: 3.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.137043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104498 restraints weight = 10942.078| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.40 r_work: 0.3461 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5825 Z= 0.175 Angle : 0.540 7.359 8237 Z= 0.286 Chirality : 0.036 0.123 951 Planarity : 0.004 0.028 803 Dihedral : 21.790 78.340 1558 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.34 % Allowed : 18.38 % Favored : 78.28 % 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 aren not related in a simple way. whole: 1.86 (0.38), residues: 510 helix: 2.36 (0.33), residues: 262 sheet: 1.38 (0.65), residues: 69 loop : -0.57 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 512 TYR 0.020 0.002 TYR A 576 PHE 0.007 0.001 PHE A 582 TRP 0.012 0.001 TRP A 442 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5821) covalent geometry : angle 0.52809 ( 8234) hydrogen bonds : bond 0.04449 ( 320) hydrogen bonds : angle 3.73083 ( 861) metal coordination : bond 0.02091 ( 4) metal coordination : angle 5.83195 ( 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 62 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7616 (mm) REVERT: A 177 LYS cc_start: 0.7799 (mmmm) cc_final: 0.7476 (tptp) REVERT: A 340 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8897 (mm) REVERT: A 365 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7687 (mm) REVERT: A 394 LEU cc_start: 0.8476 (tp) cc_final: 0.8173 (pp) REVERT: A 457 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8156 (mtm110) outliers start: 14 outliers final: 10 residues processed: 60 average time/residue: 0.1132 time to fit residues: 8.2833 Evaluate side-chains 59 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 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 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 581 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.136771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103669 restraints weight = 11263.831| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.48 r_work: 0.3444 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5825 Z= 0.212 Angle : 0.574 7.083 8237 Z= 0.304 Chirality : 0.038 0.131 951 Planarity : 0.004 0.029 803 Dihedral : 21.778 78.462 1558 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.34 % Allowed : 18.85 % 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 aren not related in a simple way. whole: 1.74 (0.38), residues: 510 helix: 2.25 (0.33), residues: 262 sheet: 1.37 (0.65), residues: 69 loop : -0.62 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 512 TYR 0.025 0.002 TYR A 576 PHE 0.007 0.001 PHE A 582 TRP 0.011 0.001 TRP A 442 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 5821) covalent geometry : angle 0.56500 ( 8234) hydrogen bonds : bond 0.04615 ( 320) hydrogen bonds : angle 3.79574 ( 861) metal coordination : bond 0.02232 ( 4) metal coordination : angle 5.47834 ( 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 60 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7453 (mm) REVERT: A 340 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8924 (mm) REVERT: A 365 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7666 (mm) REVERT: A 394 LEU cc_start: 0.8477 (tp) cc_final: 0.8177 (pp) REVERT: A 457 ARG cc_start: 0.8618 (ttm-80) cc_final: 0.8195 (mtm110) outliers start: 14 outliers final: 11 residues processed: 58 average time/residue: 0.1051 time to fit residues: 7.5954 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 : 0.163 ------------------------------------------------------------------------------- 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 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 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 581 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 21 optimal weight: 0.0770 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.136924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.104473 restraints weight = 11077.193| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.40 r_work: 0.3454 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3089 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= 0.190 Angle : 0.560 7.164 8237 Z= 0.296 Chirality : 0.037 0.127 951 Planarity : 0.004 0.028 803 Dihedral : 21.729 78.256 1558 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.34 % Allowed : 18.85 % 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 aren not related in a simple way. whole: 1.75 (0.38), residues: 510 helix: 2.25 (0.33), residues: 262 sheet: 1.37 (0.65), residues: 69 loop : -0.60 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 512 TYR 0.023 0.002 TYR A 576 PHE 0.007 0.001 PHE A 582 TRP 0.012 0.001 TRP A 442 HIS 0.003 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5821) covalent geometry : angle 0.55079 ( 8234) hydrogen bonds : bond 0.04456 ( 320) hydrogen bonds : angle 3.73096 ( 861) metal coordination : bond 0.01961 ( 4) metal coordination : angle 5.41184 ( 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 61 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7504 (mm) REVERT: A 218 ARG cc_start: 0.8450 (ptt-90) cc_final: 0.8196 (ptt-90) REVERT: A 340 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8936 (mm) REVERT: A 365 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7697 (mm) REVERT: A 394 LEU cc_start: 0.8427 (tp) cc_final: 0.8130 (pp) REVERT: A 402 TYR cc_start: 0.5937 (t80) cc_final: 0.5387 (t80) REVERT: A 457 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8184 (mtm110) REVERT: A 563 LEU cc_start: 0.8408 (mt) cc_final: 0.8161 (pp) outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 0.1029 time to fit residues: 7.5083 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 : 0.170 ------------------------------------------------------------------------------- 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 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 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 581 SER 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: 0.9980 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 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: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.137088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103103 restraints weight = 11178.241| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.61 r_work: 0.3401 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5825 Z= 0.148 Angle : 0.540 7.092 8237 Z= 0.286 Chirality : 0.036 0.126 951 Planarity : 0.004 0.027 803 Dihedral : 21.655 77.820 1558 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.39 % Allowed : 19.81 % 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 aren not related in a simple way. whole: 1.91 (0.38), residues: 510 helix: 2.38 (0.33), residues: 262 sheet: 1.40 (0.65), residues: 69 loop : -0.50 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 512 TYR 0.022 0.002 TYR A 576 PHE 0.005 0.001 PHE A 582 TRP 0.019 0.002 TRP A 415 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5821) covalent geometry : angle 0.53181 ( 8234) hydrogen bonds : bond 0.04148 ( 320) hydrogen bonds : angle 3.62251 ( 861) metal coordination : bond 0.02208 ( 4) metal coordination : angle 5.07351 ( 3) =============================================================================== Job complete usr+sys time: 1354.58 seconds wall clock time: 23 minutes 48.17 seconds (1428.17 seconds total)