Starting phenix.real_space_refine on Wed Apr 30 00:40:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0p_39710/04_2025/8z0p_39710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0p_39710/04_2025/8z0p_39710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0p_39710/04_2025/8z0p_39710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0p_39710/04_2025/8z0p_39710.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0p_39710/04_2025/8z0p_39710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0p_39710/04_2025/8z0p_39710.cif" } resolution = 3.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 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 2 6.06 5 P 1 5.49 5 S 34 5.16 5 C 2944 2.51 5 N 800 2.21 5 O 838 1.98 5 H 4627 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9246 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 9239 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 34, 'TRANS': 551} Chain breaks: 6 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.79, per 1000 atoms: 0.52 Number of scatterers: 9246 At special positions: 0 Unit cell: (67.854, 74.166, 93.628, 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 2 29.99 S 34 16.00 P 1 15.00 O 838 8.00 N 800 7.00 C 2944 6.00 H 4627 1.00 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: 2.22 Conformation dependent library (CDL) restraints added in 711.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 548 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 551 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 724 " 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1110 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 7 sheets defined 32.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.890A pdb=" N LEU A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 removed outlier: 4.267A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.848A pdb=" N ARG A 328 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 4.428A pdb=" N VAL A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 442 through 451 Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 595 removed outlier: 4.302A pdb=" N TRP A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 600 No H-bonds generated for 'chain 'A' and resid 598 through 600' Processing helix chain 'A' and resid 608 through 611 removed outlier: 3.739A pdb=" N GLN A 611 " --> pdb=" O LYS A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 611' Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.713A pdb=" N LEU A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 removed outlier: 3.643A pdb=" N ARG A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 704 through 715 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 762 Processing helix chain 'A' and resid 763 through 771 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 75 removed outlier: 6.468A pdb=" N ALA A 73 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU A 60 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 424 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 109 Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 185 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.210A pdb=" N VAL A 340 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS A 367 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 510 through 512 removed outlier: 6.455A pdb=" N THR A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ALA A 501 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A 750 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 543 removed outlier: 6.367A pdb=" N VAL A 542 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU A 576 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE A 605 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 578 " --> pdb=" O ILE A 605 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 634 through 641 removed outlier: 7.165A pdb=" N VAL A 654 " --> pdb=" O GLU A 635 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE A 637 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 652 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR A 639 " --> pdb=" O GLY A 650 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 650 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS A 660 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILE A 684 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 662 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLU A 686 " --> pdb=" O VAL A 662 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4609 1.03 - 1.22: 18 1.22 - 1.42: 1940 1.42 - 1.61: 2730 1.61 - 1.81: 50 Bond restraints: 9347 Sorted by residual: bond pdb=" N THR A 57 " pdb=" CA THR A 57 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N THR A 57 " pdb=" H THR A 57 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" N HIS A 644 " pdb=" CA HIS A 644 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" CA THR A 701 " pdb=" C THR A 701 " ideal model delta sigma weight residual 1.530 1.518 0.012 1.10e-02 8.26e+03 1.14e+00 bond pdb=" CA GLU A 174 " pdb=" C GLU A 174 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.93e-01 ... (remaining 9342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 16463 1.55 - 3.11: 417 3.11 - 4.66: 39 4.66 - 6.22: 3 6.22 - 7.77: 1 Bond angle restraints: 16923 Sorted by residual: angle pdb=" N GLU A 176 " pdb=" CA GLU A 176 " pdb=" CB GLU A 176 " ideal model delta sigma weight residual 114.17 109.02 5.15 1.14e+00 7.69e-01 2.04e+01 angle pdb=" C LEU A 514 " pdb=" CA LEU A 514 " pdb=" CB LEU A 514 " ideal model delta sigma weight residual 116.34 110.86 5.48 1.40e+00 5.10e-01 1.53e+01 angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 113.18 108.81 4.37 1.33e+00 5.65e-01 1.08e+01 angle pdb=" C LYS A 495 " pdb=" N ILE A 496 " pdb=" CA ILE A 496 " ideal model delta sigma weight residual 123.16 119.84 3.32 1.06e+00 8.90e-01 9.83e+00 angle pdb=" N LYS A 146 " pdb=" CA LYS A 146 " pdb=" C LYS A 146 " ideal model delta sigma weight residual 113.41 109.59 3.82 1.22e+00 6.72e-01 9.80e+00 ... (remaining 16918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3949 17.95 - 35.91: 322 35.91 - 53.86: 114 53.86 - 71.81: 23 71.81 - 89.77: 7 Dihedral angle restraints: 4415 sinusoidal: 2409 harmonic: 2006 Sorted by residual: dihedral pdb=" CA MET A 178 " pdb=" C MET A 178 " pdb=" N THR A 179 " pdb=" CA THR A 179 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA LYS A 146 " pdb=" C LYS A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA THR A 177 " pdb=" C THR A 177 " pdb=" N MET A 178 " pdb=" CA MET A 178 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 4412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 427 0.028 - 0.056: 181 0.056 - 0.084: 56 0.084 - 0.112: 48 0.112 - 0.140: 16 Chirality restraints: 728 Sorted by residual: chirality pdb=" CA VAL A 732 " pdb=" N VAL A 732 " pdb=" C VAL A 732 " pdb=" CB VAL A 732 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE A 605 " pdb=" N ILE A 605 " pdb=" C ILE A 605 " pdb=" CB ILE A 605 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 725 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 145 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C GLU A 145 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU A 145 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 146 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 764 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 765 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 765 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 765 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 133 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 134 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " -0.019 5.00e-02 4.00e+02 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 427 2.17 - 2.78: 18029 2.78 - 3.39: 24986 3.39 - 3.99: 32269 3.99 - 4.60: 50580 Nonbonded interactions: 126291 Sorted by model distance: nonbonded pdb=" O ALA A 344 " pdb="HD21 ASN A 371 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU A 89 " pdb=" HG SER A 557 " model vdw 1.618 2.450 nonbonded pdb="HE21 GLN A 318 " pdb=" OE1 GLU A 322 " model vdw 1.619 2.450 nonbonded pdb=" OD1 ASN A 86 " pdb="HD21 ASN A 117 " model vdw 1.628 2.450 nonbonded pdb=" O GLU A 130 " pdb=" HG1 THR A 131 " model vdw 1.642 2.450 ... (remaining 126286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.910 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: 0.150 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.920 Find NCS groups from input model: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 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 : 0.010 0.620 4723 Z= 0.349 Angle : 0.677 7.771 6399 Z= 0.394 Chirality : 0.043 0.140 728 Planarity : 0.004 0.035 820 Dihedral : 15.657 89.767 1739 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.52 % Favored : 91.78 % Rotamer: Outliers : 1.17 % Allowed : 12.50 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.36), residues: 572 helix: -0.16 (0.43), residues: 169 sheet: 0.14 (0.45), residues: 121 loop : -1.55 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 659 HIS 0.004 0.001 HIS A 644 PHE 0.016 0.002 PHE A 397 TYR 0.010 0.002 TYR A 329 ARG 0.003 0.001 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.19398 ( 136) hydrogen bonds : angle 7.40235 ( 387) metal coordination : bond 0.37142 ( 3) covalent geometry : bond 0.00317 ( 4720) covalent geometry : angle 0.67717 ( 6399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 PHE cc_start: 0.7915 (m-10) cc_final: 0.7585 (m-10) REVERT: A 623 ARG cc_start: 0.4130 (OUTLIER) cc_final: 0.3554 (ptm-80) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.4455 time to fit residues: 38.3660 Evaluate side-chains 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 623 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.206096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.187801 restraints weight = 15430.693| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.04 r_work: 0.4107 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4723 Z= 0.113 Angle : 0.577 7.869 6399 Z= 0.302 Chirality : 0.044 0.158 728 Planarity : 0.004 0.034 820 Dihedral : 6.046 40.901 633 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.34 % Favored : 91.96 % Rotamer: Outliers : 0.78 % Allowed : 12.89 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.37), residues: 572 helix: 0.37 (0.44), residues: 165 sheet: 0.15 (0.47), residues: 115 loop : -1.59 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 659 HIS 0.004 0.001 HIS A 600 PHE 0.012 0.001 PHE A 306 TYR 0.007 0.001 TYR A 329 ARG 0.002 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 136) hydrogen bonds : angle 5.63607 ( 387) metal coordination : bond 0.01117 ( 3) covalent geometry : bond 0.00263 ( 4720) covalent geometry : angle 0.57659 ( 6399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7503 (p0) cc_final: 0.7235 (p0) REVERT: A 397 PHE cc_start: 0.7980 (m-80) cc_final: 0.7646 (m-10) REVERT: A 630 ARG cc_start: 0.7136 (tmm-80) cc_final: 0.6649 (ttp80) outliers start: 4 outliers final: 1 residues processed: 71 average time/residue: 0.4457 time to fit residues: 40.9830 Evaluate side-chains 61 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.203067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.185639 restraints weight = 15660.184| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 1.98 r_work: 0.4087 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4723 Z= 0.113 Angle : 0.552 7.730 6399 Z= 0.288 Chirality : 0.043 0.141 728 Planarity : 0.004 0.036 820 Dihedral : 5.183 25.997 622 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.74 % Favored : 90.56 % Rotamer: Outliers : 1.56 % Allowed : 13.28 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.37), residues: 572 helix: 0.78 (0.45), residues: 160 sheet: -0.08 (0.46), residues: 117 loop : -1.44 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 659 HIS 0.005 0.001 HIS A 600 PHE 0.013 0.001 PHE A 306 TYR 0.008 0.001 TYR A 329 ARG 0.002 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 136) hydrogen bonds : angle 5.08071 ( 387) metal coordination : bond 0.00540 ( 3) covalent geometry : bond 0.00263 ( 4720) covalent geometry : angle 0.55247 ( 6399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7426 (p0) cc_final: 0.7189 (p0) REVERT: A 143 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6343 (mp10) REVERT: A 397 PHE cc_start: 0.8072 (m-80) cc_final: 0.7841 (m-10) REVERT: A 416 MET cc_start: 0.7201 (tmm) cc_final: 0.6808 (ttt) REVERT: A 623 ARG cc_start: 0.4385 (OUTLIER) cc_final: 0.3838 (ptt90) REVERT: A 630 ARG cc_start: 0.7098 (tmm-80) cc_final: 0.6709 (ttp80) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.4339 time to fit residues: 38.6952 Evaluate side-chains 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.193922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.177192 restraints weight = 15710.638| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.94 r_work: 0.4006 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4723 Z= 0.171 Angle : 0.621 7.803 6399 Z= 0.329 Chirality : 0.045 0.168 728 Planarity : 0.005 0.038 820 Dihedral : 5.556 22.530 622 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.27 % Favored : 90.03 % Rotamer: Outliers : 2.73 % Allowed : 13.67 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.36), residues: 572 helix: 0.13 (0.43), residues: 166 sheet: -0.40 (0.47), residues: 112 loop : -1.78 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 659 HIS 0.007 0.001 HIS A 601 PHE 0.018 0.002 PHE A 306 TYR 0.011 0.002 TYR A 425 ARG 0.003 0.001 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 136) hydrogen bonds : angle 5.17782 ( 387) metal coordination : bond 0.00215 ( 3) covalent geometry : bond 0.00410 ( 4720) covalent geometry : angle 0.62101 ( 6399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.6209 (mp10) REVERT: A 306 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6579 (m-80) REVERT: A 416 MET cc_start: 0.7166 (tmm) cc_final: 0.6838 (ttt) REVERT: A 465 ARG cc_start: 0.5729 (mtm-85) cc_final: 0.5497 (mtm-85) REVERT: A 495 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7412 (ptmm) REVERT: A 623 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.4300 (ptt90) REVERT: A 630 ARG cc_start: 0.7101 (tmm-80) cc_final: 0.6759 (ttp80) outliers start: 14 outliers final: 5 residues processed: 77 average time/residue: 0.4117 time to fit residues: 40.0608 Evaluate side-chains 70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.196988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.180065 restraints weight = 15592.640| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.91 r_work: 0.4037 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4723 Z= 0.135 Angle : 0.578 9.705 6399 Z= 0.301 Chirality : 0.044 0.162 728 Planarity : 0.004 0.036 820 Dihedral : 5.318 24.620 621 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.09 % Favored : 90.21 % Rotamer: Outliers : 2.34 % Allowed : 14.84 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.36), residues: 572 helix: 0.16 (0.43), residues: 172 sheet: -0.76 (0.46), residues: 119 loop : -1.91 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.005 0.001 HIS A 601 PHE 0.014 0.001 PHE A 306 TYR 0.007 0.001 TYR A 480 ARG 0.002 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 136) hydrogen bonds : angle 5.05345 ( 387) metal coordination : bond 0.00152 ( 3) covalent geometry : bond 0.00317 ( 4720) covalent geometry : angle 0.57833 ( 6399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 416 MET cc_start: 0.7127 (tmm) cc_final: 0.6912 (ttt) REVERT: A 465 ARG cc_start: 0.5731 (mtm-85) cc_final: 0.5524 (mtm-85) REVERT: A 623 ARG cc_start: 0.4967 (OUTLIER) cc_final: 0.4349 (ptt90) REVERT: A 630 ARG cc_start: 0.7019 (tmm-80) cc_final: 0.6705 (ttp80) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.4498 time to fit residues: 39.3436 Evaluate side-chains 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.192521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175718 restraints weight = 15816.249| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.92 r_work: 0.3997 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4723 Z= 0.178 Angle : 0.622 8.400 6399 Z= 0.328 Chirality : 0.045 0.158 728 Planarity : 0.005 0.037 820 Dihedral : 5.552 22.440 621 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.79 % Favored : 89.34 % Rotamer: Outliers : 3.32 % Allowed : 14.26 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.35), residues: 572 helix: -0.10 (0.41), residues: 173 sheet: -0.86 (0.47), residues: 121 loop : -2.11 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 659 HIS 0.007 0.001 HIS A 601 PHE 0.019 0.002 PHE A 306 TYR 0.011 0.002 TYR A 329 ARG 0.003 0.001 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 136) hydrogen bonds : angle 5.14428 ( 387) metal coordination : bond 0.00255 ( 3) covalent geometry : bond 0.00427 ( 4720) covalent geometry : angle 0.62208 ( 6399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.6551 (mp10) REVERT: A 246 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7703 (tmmt) REVERT: A 306 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: A 417 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 495 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7377 (ptmm) REVERT: A 623 ARG cc_start: 0.5237 (OUTLIER) cc_final: 0.4576 (ptt90) REVERT: A 630 ARG cc_start: 0.7031 (tmm-80) cc_final: 0.6727 (ttp80) outliers start: 17 outliers final: 8 residues processed: 71 average time/residue: 0.4688 time to fit residues: 40.8140 Evaluate side-chains 72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.190452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.173615 restraints weight = 15905.620| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.92 r_work: 0.3972 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4723 Z= 0.149 Angle : 0.589 8.162 6399 Z= 0.309 Chirality : 0.044 0.165 728 Planarity : 0.004 0.037 820 Dihedral : 5.457 24.089 621 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.39 % Favored : 90.73 % Rotamer: Outliers : 2.73 % Allowed : 15.62 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.85 (0.36), residues: 572 helix: -0.14 (0.41), residues: 179 sheet: -0.90 (0.47), residues: 119 loop : -2.14 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.005 0.001 HIS A 601 PHE 0.015 0.001 PHE A 306 TYR 0.008 0.001 TYR A 75 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 136) hydrogen bonds : angle 5.07245 ( 387) metal coordination : bond 0.00214 ( 3) covalent geometry : bond 0.00350 ( 4720) covalent geometry : angle 0.58874 ( 6399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7682 (tmmt) REVERT: A 417 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8540 (p) REVERT: A 495 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7267 (ptmm) REVERT: A 623 ARG cc_start: 0.5280 (OUTLIER) cc_final: 0.4622 (ptt90) REVERT: A 630 ARG cc_start: 0.7002 (tmm-80) cc_final: 0.6707 (ttp80) REVERT: A 699 GLU cc_start: 0.7689 (tt0) cc_final: 0.7298 (tt0) outliers start: 14 outliers final: 7 residues processed: 71 average time/residue: 0.4686 time to fit residues: 40.7079 Evaluate side-chains 73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.194843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.178809 restraints weight = 15812.041| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.78 r_work: 0.4009 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4723 Z= 0.144 Angle : 0.589 8.122 6399 Z= 0.309 Chirality : 0.044 0.151 728 Planarity : 0.004 0.037 820 Dihedral : 5.365 21.207 621 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.79 % Favored : 89.34 % Rotamer: Outliers : 2.93 % Allowed : 16.02 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.75 (0.36), residues: 572 helix: -0.02 (0.41), residues: 179 sheet: -0.87 (0.48), residues: 119 loop : -2.09 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.005 0.001 HIS A 601 PHE 0.016 0.001 PHE A 306 TYR 0.007 0.001 TYR A 75 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 136) hydrogen bonds : angle 4.98376 ( 387) metal coordination : bond 0.00168 ( 3) covalent geometry : bond 0.00341 ( 4720) covalent geometry : angle 0.58861 ( 6399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.6778 (mp10) REVERT: A 246 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7789 (tmmt) REVERT: A 417 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8497 (p) REVERT: A 495 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7403 (ptmm) REVERT: A 623 ARG cc_start: 0.5480 (OUTLIER) cc_final: 0.4863 (ptt90) REVERT: A 630 ARG cc_start: 0.6971 (tmm-80) cc_final: 0.6624 (ttp80) REVERT: A 699 GLU cc_start: 0.7757 (tt0) cc_final: 0.7439 (tt0) outliers start: 15 outliers final: 6 residues processed: 70 average time/residue: 0.4835 time to fit residues: 41.4743 Evaluate side-chains 72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN A 434 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.191145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174515 restraints weight = 15655.208| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.87 r_work: 0.3979 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4723 Z= 0.180 Angle : 0.634 7.992 6399 Z= 0.333 Chirality : 0.045 0.159 728 Planarity : 0.005 0.037 820 Dihedral : 5.602 24.617 621 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.27 % Favored : 89.86 % Rotamer: Outliers : 3.12 % Allowed : 16.21 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.98 (0.35), residues: 572 helix: -0.25 (0.41), residues: 179 sheet: -0.93 (0.49), residues: 120 loop : -2.25 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 659 HIS 0.006 0.001 HIS A 601 PHE 0.018 0.002 PHE A 306 TYR 0.008 0.002 TYR A 59 ARG 0.004 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 136) hydrogen bonds : angle 5.13717 ( 387) metal coordination : bond 0.00263 ( 3) covalent geometry : bond 0.00430 ( 4720) covalent geometry : angle 0.63433 ( 6399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.6642 (mp10) REVERT: A 246 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7747 (tmmt) REVERT: A 354 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.4830 (m-80) REVERT: A 417 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8636 (p) REVERT: A 495 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7293 (ptmm) REVERT: A 623 ARG cc_start: 0.5571 (OUTLIER) cc_final: 0.4917 (ptt90) REVERT: A 630 ARG cc_start: 0.6975 (tmm-80) cc_final: 0.6635 (ttp80) REVERT: A 699 GLU cc_start: 0.7769 (tt0) cc_final: 0.7415 (tt0) REVERT: A 700 LYS cc_start: 0.7643 (mtpt) cc_final: 0.7397 (mtpt) outliers start: 16 outliers final: 8 residues processed: 69 average time/residue: 0.4934 time to fit residues: 41.3299 Evaluate side-chains 73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.195544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178732 restraints weight = 15777.541| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.89 r_work: 0.4022 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4723 Z= 0.102 Angle : 0.558 7.991 6399 Z= 0.290 Chirality : 0.043 0.156 728 Planarity : 0.004 0.036 820 Dihedral : 5.175 20.749 621 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.22 % Favored : 90.91 % Rotamer: Outliers : 1.76 % Allowed : 17.77 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.37), residues: 572 helix: 0.29 (0.43), residues: 173 sheet: -0.77 (0.50), residues: 119 loop : -2.10 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.003 0.001 HIS A 644 PHE 0.011 0.001 PHE A 306 TYR 0.010 0.001 TYR A 75 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 136) hydrogen bonds : angle 4.83826 ( 387) metal coordination : bond 0.00071 ( 3) covalent geometry : bond 0.00239 ( 4720) covalent geometry : angle 0.55754 ( 6399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 354 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.4741 (m-80) REVERT: A 495 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7308 (ptmm) REVERT: A 623 ARG cc_start: 0.5490 (OUTLIER) cc_final: 0.4867 (ptt90) REVERT: A 630 ARG cc_start: 0.6925 (tmm-80) cc_final: 0.6595 (ttp80) REVERT: A 699 GLU cc_start: 0.7779 (tt0) cc_final: 0.7420 (tt0) outliers start: 9 outliers final: 6 residues processed: 65 average time/residue: 0.5377 time to fit residues: 42.4272 Evaluate side-chains 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.194409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177688 restraints weight = 15716.008| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.89 r_work: 0.4012 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3887 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4723 Z= 0.124 Angle : 0.568 7.872 6399 Z= 0.295 Chirality : 0.043 0.155 728 Planarity : 0.004 0.037 820 Dihedral : 5.177 23.034 621 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.92 % Favored : 90.21 % Rotamer: Outliers : 2.34 % Allowed : 17.38 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.37), residues: 572 helix: 0.27 (0.42), residues: 173 sheet: -0.78 (0.50), residues: 119 loop : -2.09 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.004 0.001 HIS A 601 PHE 0.012 0.001 PHE A 306 TYR 0.008 0.001 TYR A 75 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 136) hydrogen bonds : angle 4.82264 ( 387) metal coordination : bond 0.00144 ( 3) covalent geometry : bond 0.00297 ( 4720) covalent geometry : angle 0.56808 ( 6399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5687.90 seconds wall clock time: 98 minutes 42.79 seconds (5922.79 seconds total)