Starting phenix.real_space_refine on Sat Dec 28 20:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0p_39710/12_2024/8z0p_39710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0p_39710/12_2024/8z0p_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_39710/12_2024/8z0p_39710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0p_39710/12_2024/8z0p_39710.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0p_39710/12_2024/8z0p_39710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0p_39710/12_2024/8z0p_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.19, per 1000 atoms: 0.56 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: 2.40 Conformation dependent library (CDL) restraints added in 763.9 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: 0.78 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: 3.29 Time building geometry restraints manager: 2.86 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: 1.160 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: 0.140 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.080 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.010 ------------------------------------------------------------------------------- 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 : 0.003 0.032 4720 Z= 0.208 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 *********************** 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 : 0.644 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: 0.4441 time to fit residues: 38.2639 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 : 0.739 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 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 4720 Z= 0.172 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 *********************** 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 : 0.729 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7498 (p0) cc_final: 0.7240 (p0) REVERT: A 397 PHE cc_start: 0.7975 (m-80) cc_final: 0.7626 (m-10) REVERT: A 630 ARG cc_start: 0.7122 (tmm-80) cc_final: 0.6636 (ttp80) outliers start: 4 outliers final: 1 residues processed: 71 average time/residue: 0.3944 time to fit residues: 35.7090 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 : 1.297 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4720 Z= 0.192 Angle : 0.568 7.702 6399 Z= 0.297 Chirality : 0.044 0.142 728 Planarity : 0.004 0.036 820 Dihedral : 5.285 25.874 622 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.27 % Favored : 90.03 % Rotamer: Outliers : 1.76 % Allowed : 13.48 % Favored : 84.77 % 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: -0.89 (0.37), residues: 572 helix: 0.66 (0.45), residues: 160 sheet: -0.22 (0.47), residues: 112 loop : -1.46 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.005 0.001 HIS A 600 PHE 0.014 0.001 PHE A 306 TYR 0.008 0.001 TYR A 329 ARG 0.003 0.000 ARG A 68 *********************** 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 77 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7430 (p0) cc_final: 0.7203 (p0) REVERT: A 143 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6276 (mp10) REVERT: A 416 MET cc_start: 0.7204 (tmm) cc_final: 0.6813 (ttt) REVERT: A 623 ARG cc_start: 0.4467 (OUTLIER) cc_final: 0.3909 (ptt90) REVERT: A 630 ARG cc_start: 0.7078 (tmm-80) cc_final: 0.6700 (ttp80) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.3912 time to fit residues: 36.1785 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 : 0.622 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 418 GLN A 434 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 4720 Z= 0.308 Angle : 0.673 7.972 6399 Z= 0.359 Chirality : 0.047 0.195 728 Planarity : 0.005 0.046 820 Dihedral : 5.827 22.310 621 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.62 % Favored : 89.69 % Rotamer: Outliers : 3.12 % Allowed : 13.28 % 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: -1.81 (0.35), residues: 572 helix: -0.28 (0.41), residues: 167 sheet: -0.78 (0.46), residues: 121 loop : -1.97 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 659 HIS 0.011 0.002 HIS A 601 PHE 0.022 0.002 PHE A 306 TYR 0.014 0.002 TYR A 425 ARG 0.003 0.001 ARG A 68 *********************** 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 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.5988 (mp10) REVERT: A 246 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7757 (tmmt) REVERT: A 306 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: A 416 MET cc_start: 0.7148 (tmm) cc_final: 0.6921 (ttt) REVERT: A 465 ARG cc_start: 0.5691 (mtm-85) cc_final: 0.5489 (mtm-85) REVERT: A 495 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7413 (ptmm) REVERT: A 623 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.4457 (ptt90) REVERT: A 630 ARG cc_start: 0.7050 (tmm-80) cc_final: 0.6731 (ttp80) outliers start: 16 outliers final: 7 residues processed: 78 average time/residue: 0.4400 time to fit residues: 42.3224 Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 187 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 387 THR 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 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.0000 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 32 optimal weight: 4.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4720 Z= 0.180 Angle : 0.573 9.463 6399 Z= 0.298 Chirality : 0.043 0.161 728 Planarity : 0.004 0.036 820 Dihedral : 5.385 24.074 621 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.22 % Favored : 90.91 % Rotamer: Outliers : 1.95 % Allowed : 15.04 % Favored : 83.01 % 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: -1.59 (0.36), residues: 572 helix: 0.09 (0.42), residues: 172 sheet: -0.84 (0.46), residues: 119 loop : -1.89 (0.38), residues: 281 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 0.014 0.001 PHE A 306 TYR 0.008 0.001 TYR A 75 ARG 0.005 0.000 ARG A 328 *********************** 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 71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7411 (p0) cc_final: 0.7156 (p0) REVERT: A 417 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 623 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4392 (ptt90) REVERT: A 630 ARG cc_start: 0.6978 (tmm-80) cc_final: 0.6675 (ttp80) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.4745 time to fit residues: 38.0097 Evaluate side-chains 67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 81 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 417 VAL 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 13 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 418 GLN A 596 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4720 Z= 0.196 Angle : 0.571 8.662 6399 Z= 0.297 Chirality : 0.044 0.158 728 Planarity : 0.004 0.037 820 Dihedral : 5.279 22.218 621 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.09 % Favored : 90.03 % Rotamer: Outliers : 2.34 % Allowed : 15.04 % Favored : 82.62 % 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: 0.21 (0.42), residues: 173 sheet: -0.90 (0.47), residues: 119 loop : -1.86 (0.38), residues: 280 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 0.007 0.001 TYR A 75 ARG 0.004 0.000 ARG A 328 *********************** 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 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7392 (p0) cc_final: 0.7139 (p0) REVERT: A 465 ARG cc_start: 0.5766 (mtm-85) cc_final: 0.5550 (mtm-85) REVERT: A 495 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7312 (ptmm) REVERT: A 623 ARG cc_start: 0.5122 (OUTLIER) cc_final: 0.4468 (ptt90) REVERT: A 630 ARG cc_start: 0.6968 (tmm-80) cc_final: 0.6674 (ttp80) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.4704 time to fit residues: 39.8379 Evaluate side-chains 70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 81 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER 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 31 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4720 Z= 0.170 Angle : 0.548 8.376 6399 Z= 0.285 Chirality : 0.043 0.156 728 Planarity : 0.004 0.036 820 Dihedral : 5.123 23.027 621 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.92 % Favored : 90.21 % Rotamer: Outliers : 2.73 % Allowed : 15.04 % Favored : 82.23 % 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: -1.38 (0.36), residues: 572 helix: 0.46 (0.43), residues: 173 sheet: -0.85 (0.47), residues: 119 loop : -1.85 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 659 HIS 0.003 0.001 HIS A 601 PHE 0.013 0.001 PHE A 306 TYR 0.008 0.001 TYR A 75 ARG 0.004 0.000 ARG A 328 *********************** 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 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7369 (p0) cc_final: 0.7125 (p0) REVERT: A 417 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8413 (p) REVERT: A 495 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7263 (ptmm) REVERT: A 623 ARG cc_start: 0.5121 (OUTLIER) cc_final: 0.4477 (ptt90) REVERT: A 630 ARG cc_start: 0.6947 (tmm-80) cc_final: 0.6656 (ttp80) outliers start: 14 outliers final: 6 residues processed: 67 average time/residue: 0.4891 time to fit residues: 39.8339 Evaluate side-chains 66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 81 ASN Chi-restraints excluded: chain A residue 178 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4720 Z= 0.227 Angle : 0.589 8.026 6399 Z= 0.308 Chirality : 0.044 0.151 728 Planarity : 0.004 0.037 820 Dihedral : 5.268 21.450 621 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.79 % Favored : 89.34 % Rotamer: Outliers : 2.73 % Allowed : 16.02 % Favored : 81.25 % 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: -1.70 (0.36), residues: 572 helix: 0.07 (0.41), residues: 179 sheet: -0.88 (0.48), residues: 119 loop : -2.08 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.006 0.001 HIS A 601 PHE 0.016 0.001 PHE A 306 TYR 0.009 0.002 TYR A 329 ARG 0.004 0.000 ARG A 328 *********************** 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: 14 poor density : 62 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7381 (p0) cc_final: 0.7123 (p0) REVERT: A 143 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6913 (mp10) REVERT: A 417 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8496 (p) REVERT: A 495 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7331 (ptmm) REVERT: A 623 ARG cc_start: 0.5282 (OUTLIER) cc_final: 0.4631 (ptt90) REVERT: A 630 ARG cc_start: 0.6942 (tmm-80) cc_final: 0.6661 (ttp80) REVERT: A 699 GLU cc_start: 0.7719 (tt0) cc_final: 0.7349 (tt0) outliers start: 14 outliers final: 8 residues processed: 69 average time/residue: 0.5034 time to fit residues: 42.7999 Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4720 Z= 0.156 Angle : 0.545 7.925 6399 Z= 0.282 Chirality : 0.043 0.152 728 Planarity : 0.004 0.037 820 Dihedral : 5.028 22.195 621 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.39 % Favored : 90.73 % Rotamer: Outliers : 2.34 % Allowed : 16.60 % 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: -1.32 (0.37), residues: 572 helix: 0.50 (0.43), residues: 173 sheet: -0.72 (0.49), residues: 119 loop : -1.86 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 659 HIS 0.004 0.001 HIS A 644 PHE 0.011 0.001 PHE A 306 TYR 0.009 0.001 TYR A 75 ARG 0.003 0.000 ARG A 328 *********************** 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: 12 poor density : 63 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7362 (p0) cc_final: 0.7129 (p0) REVERT: A 417 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 495 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7234 (ptmm) REVERT: A 623 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.4612 (ptt90) REVERT: A 630 ARG cc_start: 0.6906 (tmm-80) cc_final: 0.6622 (ttp80) REVERT: A 699 GLU cc_start: 0.7705 (tt0) cc_final: 0.7351 (tt0) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.4930 time to fit residues: 40.2128 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 : 0.791 ------------------------------------------------------------------------------- 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 81 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 246 LYS 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 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4720 Z= 0.221 Angle : 0.586 7.921 6399 Z= 0.305 Chirality : 0.044 0.154 728 Planarity : 0.004 0.037 820 Dihedral : 5.171 21.713 621 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.62 % Favored : 89.51 % Rotamer: Outliers : 2.93 % Allowed : 16.41 % 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: -1.50 (0.36), residues: 572 helix: 0.37 (0.42), residues: 173 sheet: -0.75 (0.49), residues: 119 loop : -2.02 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 591 ARG 0.004 0.000 ARG A 328 ********************** 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 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7355 (p0) cc_final: 0.7119 (p0) REVERT: A 354 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.4757 (m-80) REVERT: A 417 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 495 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7303 (ptmm) REVERT: A 623 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.4725 (ptt90) REVERT: A 630 ARG cc_start: 0.6926 (tmm-80) cc_final: 0.6599 (ttp80) REVERT: A 699 GLU cc_start: 0.7711 (tt0) cc_final: 0.7350 (tt0) outliers start: 15 outliers final: 9 residues processed: 66 average time/residue: 0.4808 time to fit residues: 39.1789 Evaluate side-chains 71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 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 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.196609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.179674 restraints weight = 15497.740| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.89 r_work: 0.4031 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4720 Z= 0.163 Angle : 0.560 7.809 6399 Z= 0.288 Chirality : 0.043 0.152 728 Planarity : 0.004 0.037 820 Dihedral : 5.000 22.147 621 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.57 % Favored : 90.56 % Rotamer: Outliers : 2.34 % Allowed : 16.99 % 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: -1.36 (0.37), residues: 572 helix: 0.43 (0.43), residues: 173 sheet: -0.64 (0.50), residues: 119 loop : -1.91 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 659 HIS 0.004 0.001 HIS A 114 PHE 0.011 0.001 PHE A 306 TYR 0.009 0.001 TYR A 75 ARG 0.005 0.000 ARG A 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.56 seconds wall clock time: 55 minutes 15.89 seconds (3315.89 seconds total)