Starting phenix.real_space_refine on Tue Feb 11 13:35:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhm_34804/02_2025/8hhm_34804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhm_34804/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hhm_34804/02_2025/8hhm_34804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhm_34804/02_2025/8hhm_34804.map" model { file = "/net/cci-nas-00/data/ceres_data/8hhm_34804/02_2025/8hhm_34804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhm_34804/02_2025/8hhm_34804.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.97, per 1000 atoms: 0.71 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: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.35 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: 2.81 Time building geometry restraints manager: 1.93 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.120 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- 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 0.033 5821 Z= 0.287 Angle : 0.534 6.058 8234 Z= 0.300 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 440 HIS 0.003 0.001 HIS A 269 PHE 0.013 0.002 PHE A 582 TYR 0.009 0.001 TYR A 217 ARG 0.003 0.000 ARG A 245 *********************** 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 : 0.542 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: 0.3263 time to fit residues: 40.7737 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 : 0.507 ------------------------------------------------------------------------------- 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 48 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.143345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.108824 restraints weight = 11063.121| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.57 r_work: 0.3554 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5821 Z= 0.208 Angle : 0.532 9.514 8234 Z= 0.290 Chirality : 0.035 0.135 951 Planarity : 0.005 0.040 803 Dihedral : 21.968 78.478 1564 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.58 % Allowed : 15.99 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.39), residues: 510 helix: 2.36 (0.33), residues: 260 sheet: 1.37 (0.64), residues: 69 loop : -0.45 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 440 HIS 0.002 0.001 HIS A 7 PHE 0.007 0.001 PHE A 582 TYR 0.020 0.002 TYR A 576 ARG 0.008 0.001 ARG A 513 *********************** 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 83 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8029 (mmt) cc_final: 0.7819 (mpp) REVERT: A 340 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8807 (mm) REVERT: A 394 LEU cc_start: 0.8562 (tp) cc_final: 0.8159 (pp) REVERT: A 415 TRP cc_start: 0.7061 (m-10) cc_final: 0.6769 (m-10) REVERT: A 530 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7989 (mmm) REVERT: A 555 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6576 (m) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.2616 time to fit residues: 26.0859 Evaluate side-chains 57 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 530 MET Chi-restraints excluded: chain A residue 555 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 21 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 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 222 HIS A 452 GLN A 478 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.142552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.107330 restraints weight = 11139.271| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.56 r_work: 0.3543 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5821 Z= 0.286 Angle : 0.551 8.514 8234 Z= 0.298 Chirality : 0.037 0.146 951 Planarity : 0.005 0.050 803 Dihedral : 21.893 78.620 1561 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.82 % Allowed : 16.95 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.38), residues: 510 helix: 2.47 (0.33), residues: 260 sheet: 1.48 (0.64), residues: 69 loop : -0.66 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 442 HIS 0.008 0.001 HIS A 317 PHE 0.010 0.001 PHE A 582 TYR 0.018 0.002 TYR A 576 ARG 0.013 0.001 ARG A 513 *********************** 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: 16 poor density : 51 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8045 (mmt) cc_final: 0.7829 (mpp) REVERT: A 177 LYS cc_start: 0.8034 (mmmm) cc_final: 0.7688 (tptp) REVERT: A 340 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8810 (mm) REVERT: A 394 LEU cc_start: 0.8553 (tp) cc_final: 0.8205 (pp) outliers start: 16 outliers final: 9 residues processed: 63 average time/residue: 0.2772 time to fit residues: 21.2224 Evaluate side-chains 58 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 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 581 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.0040 chunk 40 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.144234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.110082 restraints weight = 11149.186| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.54 r_work: 0.3589 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5821 Z= 0.157 Angle : 0.495 7.809 8234 Z= 0.268 Chirality : 0.034 0.131 951 Planarity : 0.004 0.029 803 Dihedral : 21.788 77.851 1561 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.63 % Allowed : 19.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.38), residues: 510 helix: 2.51 (0.32), residues: 260 sheet: 1.70 (0.64), residues: 67 loop : -0.53 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 442 HIS 0.006 0.001 HIS A 317 PHE 0.004 0.001 PHE A 582 TYR 0.020 0.001 TYR A 576 ARG 0.008 0.001 ARG A 513 *********************** 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 70 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7970 (mmt) cc_final: 0.7734 (mpp) REVERT: A 46 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7506 (mm) REVERT: A 177 LYS cc_start: 0.8010 (mmmm) cc_final: 0.7792 (mppt) REVERT: A 340 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8814 (mm) REVERT: A 394 LEU cc_start: 0.8528 (tp) cc_final: 0.8182 (pp) REVERT: A 408 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7591 (mm-30) REVERT: A 513 ARG cc_start: 0.5043 (OUTLIER) cc_final: 0.4724 (ptm160) outliers start: 11 outliers final: 2 residues processed: 67 average time/residue: 0.2885 time to fit residues: 23.1792 Evaluate side-chains 51 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 340 ILE Chi-restraints excluded: chain A residue 513 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.143837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109014 restraints weight = 10958.899| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.54 r_work: 0.3602 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5821 Z= 0.210 Angle : 0.511 7.524 8234 Z= 0.275 Chirality : 0.035 0.162 951 Planarity : 0.004 0.034 803 Dihedral : 21.716 77.996 1558 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.06 % Allowed : 17.90 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.38), residues: 510 helix: 2.55 (0.32), residues: 260 sheet: 1.70 (0.64), residues: 67 loop : -0.58 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 442 HIS 0.008 0.001 HIS A 317 PHE 0.005 0.001 PHE A 582 TYR 0.019 0.002 TYR A 576 ARG 0.007 0.001 ARG A 513 *********************** 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 68 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8024 (mmt) cc_final: 0.7803 (mpp) REVERT: A 46 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7553 (mm) REVERT: A 177 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7786 (tptp) REVERT: A 340 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8805 (mm) REVERT: A 394 LEU cc_start: 0.8451 (tp) cc_final: 0.8113 (pp) REVERT: A 408 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7395 (mm-30) outliers start: 17 outliers final: 5 residues processed: 64 average time/residue: 0.2494 time to fit residues: 19.9774 Evaluate side-chains 49 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 340 ILE Chi-restraints excluded: chain A residue 361 VAL 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 40 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.137172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.104482 restraints weight = 10766.097| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.36 r_work: 0.3464 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5821 Z= 0.296 Angle : 0.554 7.462 8234 Z= 0.297 Chirality : 0.037 0.171 951 Planarity : 0.005 0.034 803 Dihedral : 21.741 78.337 1558 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.82 % Allowed : 18.14 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.38), residues: 510 helix: 2.44 (0.33), residues: 261 sheet: 1.61 (0.64), residues: 67 loop : -0.65 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 450 HIS 0.008 0.001 HIS A 317 PHE 0.008 0.001 PHE A 582 TYR 0.018 0.002 TYR A 576 ARG 0.009 0.001 ARG A 125 *********************** 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 71 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7653 (mm) REVERT: A 125 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8210 (mtm180) REVERT: A 177 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7476 (tptm) REVERT: A 340 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8864 (mm) REVERT: A 394 LEU cc_start: 0.8506 (tp) cc_final: 0.8185 (pp) REVERT: A 408 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 563 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8060 (mm) outliers start: 16 outliers final: 10 residues processed: 67 average time/residue: 0.2182 time to fit residues: 18.5694 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 : 0.405 ------------------------------------------------------------------------------- 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 361 VAL 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 34 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 40.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.138496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106083 restraints weight = 10806.429| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.36 r_work: 0.3482 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.003 0.025 5821 Z= 0.202 Angle : 0.518 7.042 8234 Z= 0.278 Chirality : 0.035 0.166 951 Planarity : 0.004 0.030 803 Dihedral : 21.720 77.930 1558 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.10 % Allowed : 19.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.38), residues: 510 helix: 2.43 (0.33), residues: 262 sheet: 1.64 (0.64), residues: 67 loop : -0.55 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 442 HIS 0.008 0.001 HIS A 317 PHE 0.005 0.001 PHE A 582 TYR 0.020 0.002 TYR A 576 ARG 0.006 0.000 ARG A 512 *********************** 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 61 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7620 (mm) REVERT: A 125 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8413 (mtm180) REVERT: A 177 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7391 (tptm) REVERT: A 340 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8868 (mm) REVERT: A 394 LEU cc_start: 0.8472 (tp) cc_final: 0.8169 (pp) outliers start: 13 outliers final: 8 residues processed: 58 average time/residue: 0.2333 time to fit residues: 17.5380 Evaluate side-chains 63 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 340 ILE Chi-restraints excluded: chain A residue 350 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 47 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.139260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.106284 restraints weight = 10961.566| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.44 r_work: 0.3490 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5821 Z= 0.186 Angle : 0.509 6.806 8234 Z= 0.273 Chirality : 0.035 0.151 951 Planarity : 0.004 0.029 803 Dihedral : 21.627 77.573 1558 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.39 % Allowed : 19.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.38), residues: 510 helix: 2.46 (0.33), residues: 262 sheet: 1.49 (0.64), residues: 69 loop : -0.38 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 442 HIS 0.007 0.001 HIS A 317 PHE 0.006 0.001 PHE A 582 TYR 0.022 0.002 TYR A 576 ARG 0.008 0.000 ARG A 512 *********************** 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 64 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.505 Fit side-chains REVERT: A 46 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7631 (mm) REVERT: A 125 ARG cc_start: 0.8705 (mtt180) cc_final: 0.8336 (mtm180) REVERT: A 177 LYS cc_start: 0.7947 (mmmm) cc_final: 0.7396 (tptm) REVERT: A 394 LEU cc_start: 0.8426 (tp) cc_final: 0.8136 (pp) REVERT: A 457 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8147 (mtm110) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.2585 time to fit residues: 19.4279 Evaluate side-chains 53 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 350 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 52 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.138705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.105779 restraints weight = 11048.816| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.44 r_work: 0.3482 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5821 Z= 0.218 Angle : 0.525 6.598 8234 Z= 0.283 Chirality : 0.036 0.156 951 Planarity : 0.004 0.030 803 Dihedral : 21.626 77.663 1556 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.63 % Allowed : 19.33 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.38), residues: 510 helix: 2.42 (0.33), residues: 262 sheet: 1.50 (0.63), residues: 69 loop : -0.44 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 442 HIS 0.007 0.001 HIS A 317 PHE 0.006 0.001 PHE A 582 TYR 0.027 0.002 TYR A 576 ARG 0.008 0.000 ARG A 512 *********************** 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 59 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7702 (mm) REVERT: A 125 ARG cc_start: 0.8680 (mtt180) cc_final: 0.8349 (mtm180) REVERT: A 177 LYS cc_start: 0.7947 (mmmm) cc_final: 0.7407 (tptm) REVERT: A 394 LEU cc_start: 0.8420 (tp) cc_final: 0.8135 (pp) REVERT: A 402 TYR cc_start: 0.5914 (t80) cc_final: 0.5140 (t80) REVERT: A 457 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8161 (mtm110) REVERT: A 563 LEU cc_start: 0.8416 (mt) cc_final: 0.8148 (pp) outliers start: 11 outliers final: 7 residues processed: 58 average time/residue: 0.2597 time to fit residues: 18.2979 Evaluate side-chains 55 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL 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 36 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.138265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.105279 restraints weight = 11115.263| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.46 r_work: 0.3472 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5821 Z= 0.244 Angle : 0.555 9.142 8234 Z= 0.298 Chirality : 0.036 0.160 951 Planarity : 0.004 0.029 803 Dihedral : 21.629 77.776 1556 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.91 % Allowed : 19.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.38), residues: 510 helix: 2.36 (0.33), residues: 262 sheet: 1.49 (0.63), residues: 69 loop : -0.40 (0.46), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 415 HIS 0.007 0.001 HIS A 317 PHE 0.007 0.001 PHE A 582 TYR 0.022 0.002 TYR A 576 ARG 0.010 0.001 ARG A 512 ********************** 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 57 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7686 (mm) REVERT: A 125 ARG cc_start: 0.8678 (mtt180) cc_final: 0.8322 (mtm180) REVERT: A 177 LYS cc_start: 0.7847 (mmmm) cc_final: 0.7378 (tptm) REVERT: A 394 LEU cc_start: 0.8416 (tp) cc_final: 0.8139 (pp) REVERT: A 457 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8178 (mtm110) REVERT: A 563 LEU cc_start: 0.8402 (mt) cc_final: 0.8164 (pp) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.2749 time to fit residues: 18.7436 Evaluate side-chains 54 residues out of total 419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL 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 1 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 0.0030 chunk 35 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 overall best weight: 3.7396 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.138388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.105032 restraints weight = 11208.255| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.48 r_work: 0.3468 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5821 Z= 0.239 Angle : 0.548 8.325 8234 Z= 0.293 Chirality : 0.036 0.168 951 Planarity : 0.004 0.030 803 Dihedral : 21.626 77.786 1556 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.15 % Allowed : 20.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.38), residues: 510 helix: 2.55 (0.33), residues: 256 sheet: 1.53 (0.63), residues: 69 loop : -0.35 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 415 HIS 0.006 0.001 HIS A 317 PHE 0.007 0.001 PHE A 582 TYR 0.021 0.002 TYR A 576 ARG 0.010 0.001 ARG A 512 =============================================================================== Job complete usr+sys time: 2610.60 seconds wall clock time: 47 minutes 5.88 seconds (2825.88 seconds total)