Starting phenix.real_space_refine on Mon May 12 14:09:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0p_39710/05_2025/8z0p_39710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0p_39710/05_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_39710/05_2025/8z0p_39710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0p_39710/05_2025/8z0p_39710.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0p_39710/05_2025/8z0p_39710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0p_39710/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.97, per 1000 atoms: 0.54 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: 2.59 Conformation dependent library (CDL) restraints added in 619.0 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: 0.78 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: 3.11 Time building geometry restraints manager: 3.06 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: 1.940 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: 0.170 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.490 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- 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 : 0.669 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: 0.4442 time to fit residues: 38.1058 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 : 0.650 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.187802 restraints weight = 15430.690| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.04 r_work: 0.4108 rms_B_bonded: 2.56 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 : 0.746 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7504 (p0) cc_final: 0.7235 (p0) REVERT: A 397 PHE cc_start: 0.7979 (m-80) cc_final: 0.7645 (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: 0.3923 time to fit residues: 35.2913 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 : 0.738 ------------------------------------------------------------------------------- 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: 0.8980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.204940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.186951 restraints weight = 15644.871| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.02 r_work: 0.4102 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4723 Z= 0.104 Angle : 0.543 7.831 6399 Z= 0.282 Chirality : 0.043 0.140 728 Planarity : 0.004 0.035 820 Dihedral : 5.137 26.610 622 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.69 % Favored : 91.61 % Rotamer: Outliers : 0.98 % Allowed : 14.06 % Favored : 84.96 % 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: -0.70 (0.38), residues: 572 helix: 0.86 (0.45), residues: 159 sheet: -0.05 (0.46), residues: 117 loop : -1.40 (0.40), residues: 296 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 623 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 136) hydrogen bonds : angle 5.18490 ( 387) metal coordination : bond 0.00561 ( 3) covalent geometry : bond 0.00242 ( 4720) covalent geometry : angle 0.54280 ( 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 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7436 (p0) cc_final: 0.7198 (p0) REVERT: A 397 PHE cc_start: 0.8010 (m-80) cc_final: 0.7678 (m-10) REVERT: A 416 MET cc_start: 0.7165 (tmm) cc_final: 0.6770 (ttt) REVERT: A 623 ARG cc_start: 0.4221 (OUTLIER) cc_final: 0.3701 (ptt90) REVERT: A 630 ARG cc_start: 0.7100 (tmm-80) cc_final: 0.6694 (ttp80) outliers start: 5 outliers final: 4 residues processed: 67 average time/residue: 0.4036 time to fit residues: 33.9869 Evaluate side-chains 66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 178 MET Chi-restraints excluded: chain A residue 623 ARG 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: 2.9990 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.190205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.173511 restraints weight = 15819.671| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.94 r_work: 0.3969 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 4723 Z= 0.227 Angle : 0.712 8.249 6399 Z= 0.379 Chirality : 0.048 0.180 728 Planarity : 0.006 0.055 820 Dihedral : 6.067 24.333 622 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.97 % Favored : 89.34 % Rotamer: Outliers : 2.93 % Allowed : 13.28 % Favored : 83.79 % 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: -1.90 (0.35), residues: 572 helix: -0.63 (0.40), residues: 177 sheet: -0.80 (0.47), residues: 119 loop : -1.87 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 659 HIS 0.011 0.002 HIS A 601 PHE 0.025 0.002 PHE A 306 TYR 0.015 0.003 TYR A 425 ARG 0.004 0.001 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 136) hydrogen bonds : angle 5.47256 ( 387) metal coordination : bond 0.00420 ( 3) covalent geometry : bond 0.00541 ( 4720) covalent geometry : angle 0.71172 ( 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 76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.6012 (mp10) REVERT: A 246 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7697 (tmmt) REVERT: A 306 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6595 (m-80) REVERT: A 416 MET cc_start: 0.7144 (tmm) cc_final: 0.6837 (ttt) REVERT: A 465 ARG cc_start: 0.5675 (mtm-85) cc_final: 0.5459 (mtm-85) REVERT: A 495 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7396 (ptmm) REVERT: A 623 ARG cc_start: 0.5044 (OUTLIER) cc_final: 0.4307 (ptm-80) REVERT: A 630 ARG cc_start: 0.7109 (tmm-80) cc_final: 0.6774 (ttp80) outliers start: 15 outliers final: 5 residues processed: 73 average time/residue: 0.4213 time to fit residues: 38.2593 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 : 0.713 ------------------------------------------------------------------------------- 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 246 LYS 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: 3.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN A 418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.195564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178631 restraints weight = 15627.308| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.92 r_work: 0.4025 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4723 Z= 0.128 Angle : 0.589 9.777 6399 Z= 0.308 Chirality : 0.044 0.154 728 Planarity : 0.004 0.036 820 Dihedral : 5.537 25.057 621 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.39 % Favored : 90.91 % Rotamer: Outliers : 1.37 % Allowed : 15.04 % 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: -1.62 (0.36), residues: 572 helix: -0.07 (0.42), residues: 172 sheet: -0.85 (0.47), residues: 117 loop : -1.82 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 329 ARG 0.002 0.000 ARG A 623 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 136) hydrogen bonds : angle 5.17527 ( 387) metal coordination : bond 0.00177 ( 3) covalent geometry : bond 0.00301 ( 4720) covalent geometry : angle 0.58910 ( 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 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 GLU cc_start: 0.7568 (tp30) cc_final: 0.7309 (tp30) REVERT: A 416 MET cc_start: 0.7125 (tmm) cc_final: 0.6915 (ttt) REVERT: A 465 ARG cc_start: 0.5739 (mtm-85) cc_final: 0.5529 (mtm-85) REVERT: A 630 ARG cc_start: 0.7033 (tmm-80) cc_final: 0.6713 (ttp80) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.4316 time to fit residues: 34.4453 Evaluate side-chains 66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 441 CYS 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: 0.9980 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 596 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.193359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176928 restraints weight = 15799.311| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.87 r_work: 0.3991 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4723 Z= 0.170 Angle : 0.619 8.826 6399 Z= 0.326 Chirality : 0.045 0.156 728 Planarity : 0.005 0.037 820 Dihedral : 5.602 23.136 621 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.31 % Favored : 88.81 % Rotamer: Outliers : 2.73 % Allowed : 14.65 % 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: -1.88 (0.36), residues: 572 helix: -0.29 (0.41), residues: 179 sheet: -0.93 (0.47), residues: 121 loop : -2.05 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 659 HIS 0.007 0.001 HIS A 601 PHE 0.020 0.001 PHE A 306 TYR 0.011 0.002 TYR A 329 ARG 0.007 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 136) hydrogen bonds : angle 5.19059 ( 387) metal coordination : bond 0.00214 ( 3) covalent geometry : bond 0.00404 ( 4720) covalent geometry : angle 0.61858 ( 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 78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.6587 (mp10) REVERT: A 246 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7693 (tmmt) REVERT: A 306 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: A 417 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8489 (p) REVERT: A 495 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7382 (ptmm) REVERT: A 623 ARG cc_start: 0.5262 (OUTLIER) cc_final: 0.4603 (ptt90) REVERT: A 630 ARG cc_start: 0.7033 (tmm-80) cc_final: 0.6679 (ttp80) outliers start: 14 outliers final: 7 residues processed: 72 average time/residue: 0.4547 time to fit residues: 40.0915 Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.194309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.177445 restraints weight = 15670.880| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 1.90 r_work: 0.4012 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3191 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= 0.137 Angle : 0.584 8.287 6399 Z= 0.306 Chirality : 0.044 0.148 728 Planarity : 0.004 0.036 820 Dihedral : 5.425 23.890 621 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.74 % Favored : 90.38 % Rotamer: Outliers : 1.95 % Allowed : 16.41 % 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: -1.79 (0.36), residues: 572 helix: -0.09 (0.42), residues: 179 sheet: -0.95 (0.48), residues: 119 loop : -2.06 (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 0.006 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 136) hydrogen bonds : angle 5.05733 ( 387) metal coordination : bond 0.00177 ( 3) covalent geometry : bond 0.00322 ( 4720) covalent geometry : angle 0.58445 ( 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 73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8515 (p) REVERT: A 465 ARG cc_start: 0.5909 (mtm-85) cc_final: 0.5706 (mtm-85) REVERT: A 495 LYS cc_start: 0.7619 (ptpp) cc_final: 0.7299 (ptmm) REVERT: A 623 ARG cc_start: 0.5270 (OUTLIER) cc_final: 0.4619 (ptt90) REVERT: A 630 ARG cc_start: 0.6986 (tmm-80) cc_final: 0.6633 (ttp80) REVERT: A 699 GLU cc_start: 0.7698 (tt0) cc_final: 0.7317 (tt0) outliers start: 10 outliers final: 6 residues processed: 67 average time/residue: 0.4603 time to fit residues: 37.7523 Evaluate side-chains 71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 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=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: 3.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.193359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177427 restraints weight = 15917.017| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.78 r_work: 0.3996 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4723 Z= 0.160 Angle : 0.609 8.397 6399 Z= 0.319 Chirality : 0.045 0.151 728 Planarity : 0.004 0.037 820 Dihedral : 5.492 21.727 621 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.31 % Favored : 88.81 % Rotamer: Outliers : 3.12 % Allowed : 15.62 % 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: -1.97 (0.36), residues: 572 helix: -0.31 (0.40), residues: 185 sheet: -0.98 (0.48), residues: 119 loop : -2.19 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 659 HIS 0.006 0.001 HIS A 601 PHE 0.017 0.001 PHE A 306 TYR 0.007 0.001 TYR A 480 ARG 0.004 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 136) hydrogen bonds : angle 5.07551 ( 387) metal coordination : bond 0.00214 ( 3) covalent geometry : bond 0.00382 ( 4720) covalent geometry : angle 0.60866 ( 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 78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.6727 (mp10) REVERT: A 354 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.4941 (m-80) REVERT: A 417 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8515 (p) REVERT: A 495 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7389 (ptmm) REVERT: A 623 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.4872 (ptt90) REVERT: A 630 ARG cc_start: 0.7006 (tmm-80) cc_final: 0.6665 (ttp80) REVERT: A 699 GLU cc_start: 0.7763 (tt0) cc_final: 0.7423 (tt0) outliers start: 16 outliers final: 8 residues processed: 72 average time/residue: 0.4481 time to fit residues: 39.5960 Evaluate side-chains 75 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 354 TYR 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 643 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: 2.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.195298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.179448 restraints weight = 15538.535| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.76 r_work: 0.4018 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4723 Z= 0.125 Angle : 0.577 8.027 6399 Z= 0.301 Chirality : 0.043 0.143 728 Planarity : 0.004 0.037 820 Dihedral : 5.322 22.980 621 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.92 % Favored : 90.21 % Rotamer: Outliers : 3.12 % Allowed : 16.02 % Favored : 80.86 % 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: 0.16 (0.42), residues: 173 sheet: -0.91 (0.49), residues: 119 loop : -2.08 (0.37), 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 0.014 0.001 PHE A 306 TYR 0.009 0.001 TYR A 75 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 136) hydrogen bonds : angle 4.91882 ( 387) metal coordination : bond 0.00121 ( 3) covalent geometry : bond 0.00294 ( 4720) covalent geometry : angle 0.57743 ( 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 78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6956 (mp10) REVERT: A 354 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.4887 (m-80) REVERT: A 417 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8489 (p) REVERT: A 495 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7329 (ptmm) REVERT: A 623 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.4893 (ptt90) REVERT: A 630 ARG cc_start: 0.6969 (tmm-80) cc_final: 0.6636 (ttp80) REVERT: A 699 GLU cc_start: 0.7761 (tt0) cc_final: 0.7426 (tt0) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 0.4471 time to fit residues: 38.8379 Evaluate side-chains 75 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 354 TYR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 573 LEU 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: 5.9990 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.199077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183000 restraints weight = 15718.759| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.78 r_work: 0.4054 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4723 Z= 0.095 Angle : 0.546 8.102 6399 Z= 0.281 Chirality : 0.043 0.149 728 Planarity : 0.004 0.037 820 Dihedral : 5.000 20.667 621 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.74 % Favored : 90.38 % Rotamer: Outliers : 1.95 % Allowed : 16.99 % 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: -1.42 (0.37), residues: 572 helix: 0.48 (0.43), residues: 173 sheet: -0.76 (0.49), residues: 119 loop : -1.97 (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 114 PHE 0.011 0.001 PHE A 306 TYR 0.009 0.001 TYR A 75 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.02810 ( 136) hydrogen bonds : angle 4.72398 ( 387) metal coordination : bond 0.00031 ( 3) covalent geometry : bond 0.00223 ( 4720) covalent geometry : angle 0.54581 ( 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 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.4825 (m-80) REVERT: A 417 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 495 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7311 (ptmm) REVERT: A 623 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.4831 (ptt90) REVERT: A 630 ARG cc_start: 0.6940 (tmm-80) cc_final: 0.6616 (ttp80) REVERT: A 699 GLU cc_start: 0.7697 (tt0) cc_final: 0.7384 (tt0) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.4860 time to fit residues: 38.1060 Evaluate side-chains 68 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL 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 417 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 623 ARG 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: 4.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.192702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175882 restraints weight = 15769.154| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.89 r_work: 0.3995 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4723 Z= 0.165 Angle : 0.601 7.918 6399 Z= 0.314 Chirality : 0.045 0.151 728 Planarity : 0.004 0.038 820 Dihedral : 5.307 23.203 621 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.62 % Favored : 89.51 % Rotamer: Outliers : 2.54 % Allowed : 16.60 % Favored : 80.86 % 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: -1.68 (0.36), residues: 572 helix: 0.09 (0.42), residues: 179 sheet: -0.87 (0.49), residues: 119 loop : -2.07 (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 0.015 0.001 PHE A 306 TYR 0.007 0.001 TYR A 75 ARG 0.004 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 136) hydrogen bonds : angle 4.86766 ( 387) metal coordination : bond 0.00327 ( 3) covalent geometry : bond 0.00395 ( 4720) covalent geometry : angle 0.60133 ( 6399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5247.50 seconds wall clock time: 90 minutes 39.58 seconds (5439.58 seconds total)