Starting phenix.real_space_refine on Thu Mar 13 16:47:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0p_39710/03_2025/8z0p_39710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0p_39710/03_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_39710/03_2025/8z0p_39710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0p_39710/03_2025/8z0p_39710.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0p_39710/03_2025/8z0p_39710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0p_39710/03_2025/8z0p_39710.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1 5.49 5 S 34 5.16 5 C 2944 2.51 5 N 800 2.21 5 O 838 1.98 5 H 4627 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.67, per 1000 atoms: 0.51 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: 2.28 Conformation dependent library (CDL) restraints added in 675.7 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: 0.83 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: 3.05 Time building geometry restraints manager: 2.79 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: 1.790 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: 0.160 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.850 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- 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 : 0.718 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: 0.4375 time to fit residues: 37.8124 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 : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 623 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.206096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.187801 restraints weight = 15430.693| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.04 r_work: 0.4107 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 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 : 0.626 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7503 (p0) cc_final: 0.7235 (p0) REVERT: A 397 PHE cc_start: 0.7980 (m-80) cc_final: 0.7646 (m-10) REVERT: A 630 ARG cc_start: 0.7136 (tmm-80) cc_final: 0.6649 (ttp80) outliers start: 4 outliers final: 1 residues processed: 71 average time/residue: 0.3766 time to fit residues: 33.8886 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 : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.203067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.185639 restraints weight = 15660.184| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 1.98 r_work: 0.4087 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4720 Z= 0.174 Angle : 0.552 7.730 6399 Z= 0.288 Chirality : 0.043 0.141 728 Planarity : 0.004 0.036 820 Dihedral : 5.183 25.997 622 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.74 % Favored : 90.56 % Rotamer: Outliers : 1.56 % Allowed : 13.28 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.37), residues: 572 helix: 0.78 (0.45), residues: 160 sheet: -0.08 (0.46), residues: 117 loop : -1.44 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 659 HIS 0.005 0.001 HIS A 600 PHE 0.013 0.001 PHE A 306 TYR 0.008 0.001 TYR A 329 ARG 0.002 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7426 (p0) cc_final: 0.7189 (p0) REVERT: A 143 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6343 (mp10) REVERT: A 397 PHE cc_start: 0.8072 (m-80) cc_final: 0.7841 (m-10) REVERT: A 416 MET cc_start: 0.7201 (tmm) cc_final: 0.6808 (ttt) REVERT: A 623 ARG cc_start: 0.4385 (OUTLIER) cc_final: 0.3838 (ptt90) REVERT: A 630 ARG cc_start: 0.7098 (tmm-80) cc_final: 0.6709 (ttp80) outliers start: 8 outliers final: 5 residues processed: 70 average time/residue: 0.3862 time to fit residues: 34.1400 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 : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.193922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.177192 restraints weight = 15710.638| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.94 r_work: 0.4006 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4720 Z= 0.262 Angle : 0.621 7.803 6399 Z= 0.329 Chirality : 0.045 0.168 728 Planarity : 0.005 0.038 820 Dihedral : 5.556 22.530 622 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.27 % Favored : 90.03 % Rotamer: Outliers : 2.73 % Allowed : 13.67 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.36), residues: 572 helix: 0.13 (0.43), residues: 166 sheet: -0.40 (0.47), residues: 112 loop : -1.78 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 659 HIS 0.007 0.001 HIS A 601 PHE 0.018 0.002 PHE A 306 TYR 0.011 0.002 TYR A 425 ARG 0.003 0.001 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.6209 (mp10) REVERT: A 306 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6579 (m-80) REVERT: A 416 MET cc_start: 0.7166 (tmm) cc_final: 0.6838 (ttt) REVERT: A 465 ARG cc_start: 0.5729 (mtm-85) cc_final: 0.5497 (mtm-85) REVERT: A 495 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7412 (ptmm) REVERT: A 623 ARG cc_start: 0.4866 (OUTLIER) cc_final: 0.4300 (ptt90) REVERT: A 630 ARG cc_start: 0.7101 (tmm-80) cc_final: 0.6759 (ttp80) outliers start: 14 outliers final: 5 residues processed: 77 average time/residue: 0.4016 time to fit residues: 38.7002 Evaluate side-chains 70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.198214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.181139 restraints weight = 15531.354| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.93 r_work: 0.4050 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2311 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= 0.179 Angle : 0.564 9.815 6399 Z= 0.293 Chirality : 0.043 0.157 728 Planarity : 0.004 0.036 820 Dihedral : 5.242 23.710 621 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.57 % Favored : 90.73 % Rotamer: Outliers : 2.15 % Allowed : 14.65 % Favored : 83.20 % 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: -1.37 (0.36), residues: 572 helix: 0.24 (0.43), residues: 172 sheet: -0.70 (0.46), residues: 117 loop : -1.74 (0.38), residues: 283 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 0.013 0.001 PHE A 306 TYR 0.006 0.001 TYR A 75 ARG 0.002 0.000 ARG A 623 *********************** 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: 11 poor density : 60 time to evaluate : 0.686 Fit side-chains REVERT: A 416 MET cc_start: 0.7148 (tmm) cc_final: 0.6864 (ttt) REVERT: A 465 ARG cc_start: 0.5723 (mtm-85) cc_final: 0.5505 (mtm-85) REVERT: A 495 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7306 (ptmm) REVERT: A 623 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.4249 (ptt90) REVERT: A 630 ARG cc_start: 0.7023 (tmm-80) cc_final: 0.6703 (ttp80) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.4510 time to fit residues: 36.7787 Evaluate side-chains 67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 246 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.191018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.174303 restraints weight = 15843.889| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.91 r_work: 0.3979 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4720 Z= 0.284 Angle : 0.650 8.346 6399 Z= 0.345 Chirality : 0.046 0.162 728 Planarity : 0.005 0.045 820 Dihedral : 5.694 23.122 621 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.44 % Favored : 89.69 % Rotamer: Outliers : 3.32 % Allowed : 14.45 % 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: -1.92 (0.35), residues: 572 helix: -0.31 (0.40), residues: 179 sheet: -0.91 (0.47), residues: 121 loop : -2.10 (0.37), residues: 272 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 0.010 0.002 TYR A 480 ARG 0.003 0.001 ARG A 623 *********************** 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 80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.6471 (mp10) REVERT: A 246 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7730 (tmmt) REVERT: A 306 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: A 417 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8503 (p) REVERT: A 495 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7404 (ptmm) REVERT: A 623 ARG cc_start: 0.5281 (OUTLIER) cc_final: 0.4604 (ptt90) REVERT: A 630 ARG cc_start: 0.7029 (tmm-80) cc_final: 0.6675 (ttp80) REVERT: A 699 GLU cc_start: 0.7748 (tt0) cc_final: 0.7339 (tt0) REVERT: A 721 MET cc_start: 0.7889 (tpp) cc_final: 0.7577 (mtp) outliers start: 17 outliers final: 8 residues processed: 75 average time/residue: 0.4552 time to fit residues: 42.1467 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 : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.196734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.180402 restraints weight = 15650.475| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.85 r_work: 0.4031 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4720 Z= 0.177 Angle : 0.569 8.113 6399 Z= 0.297 Chirality : 0.043 0.160 728 Planarity : 0.004 0.036 820 Dihedral : 5.336 23.450 621 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.39 % Favored : 90.73 % 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: -1.66 (0.36), residues: 572 helix: 0.06 (0.42), residues: 179 sheet: -0.89 (0.48), residues: 117 loop : -2.00 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 659 HIS 0.004 0.001 HIS A 552 PHE 0.013 0.001 PHE A 306 TYR 0.009 0.001 TYR A 329 ARG 0.007 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 71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 495 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7304 (ptmm) REVERT: A 623 ARG cc_start: 0.5236 (OUTLIER) cc_final: 0.4590 (ptt90) REVERT: A 630 ARG cc_start: 0.6980 (tmm-80) cc_final: 0.6677 (ttp80) REVERT: A 699 GLU cc_start: 0.7675 (tt0) cc_final: 0.7257 (tt0) REVERT: A 721 MET cc_start: 0.7858 (tpp) cc_final: 0.7591 (mtp) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.4946 time to fit residues: 39.7818 Evaluate side-chains 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.192211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175042 restraints weight = 15914.417| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.91 r_work: 0.3986 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4720 Z= 0.296 Angle : 0.637 8.146 6399 Z= 0.336 Chirality : 0.046 0.162 728 Planarity : 0.005 0.037 820 Dihedral : 5.653 23.231 621 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.62 % Favored : 89.51 % Rotamer: Outliers : 2.73 % Allowed : 16.21 % 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: -2.04 (0.35), residues: 572 helix: -0.38 (0.40), residues: 185 sheet: -0.91 (0.49), residues: 121 loop : -2.28 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 659 HIS 0.007 0.001 HIS A 601 PHE 0.019 0.002 PHE A 306 TYR 0.011 0.002 TYR A 329 ARG 0.003 0.001 ARG A 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 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7773 (tmmt) REVERT: A 354 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.4955 (m-80) REVERT: A 417 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 495 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7359 (ptmm) REVERT: A 623 ARG cc_start: 0.5453 (OUTLIER) cc_final: 0.4787 (ptt90) REVERT: A 630 ARG cc_start: 0.6993 (tmm-80) cc_final: 0.6654 (ttp80) REVERT: A 699 GLU cc_start: 0.7815 (tt0) cc_final: 0.7428 (tt0) outliers start: 14 outliers final: 6 residues processed: 69 average time/residue: 0.4737 time to fit residues: 39.9681 Evaluate side-chains 71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 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 654 VAL Chi-restraints excluded: chain A residue 667 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.191355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.174759 restraints weight = 15635.411| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.87 r_work: 0.3983 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4720 Z= 0.265 Angle : 0.622 8.135 6399 Z= 0.327 Chirality : 0.045 0.155 728 Planarity : 0.005 0.037 820 Dihedral : 5.632 24.066 621 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.44 % Favored : 89.69 % 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: -1.97 (0.36), residues: 572 helix: -0.25 (0.41), residues: 179 sheet: -0.98 (0.49), residues: 119 loop : -2.20 (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 0.017 0.002 PHE A 306 TYR 0.009 0.002 TYR A 59 ARG 0.005 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 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: A 246 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7758 (tmmt) REVERT: A 354 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.4910 (m-80) REVERT: A 417 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (p) REVERT: A 495 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7314 (ptmm) REVERT: A 623 ARG cc_start: 0.5573 (OUTLIER) cc_final: 0.4913 (ptt90) REVERT: A 630 ARG cc_start: 0.6970 (tmm-80) cc_final: 0.6640 (ttp80) REVERT: A 699 GLU cc_start: 0.7780 (tt0) cc_final: 0.7412 (tt0) REVERT: A 700 LYS cc_start: 0.7616 (mtpt) cc_final: 0.7373 (mtpt) outliers start: 15 outliers final: 6 residues processed: 67 average time/residue: 0.4926 time to fit residues: 39.9156 Evaluate side-chains 72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 246 LYS Chi-restraints excluded: chain A residue 354 TYR 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 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: 0.6980 chunk 25 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.199365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.183277 restraints weight = 15695.160| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.78 r_work: 0.4054 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4720 Z= 0.145 Angle : 0.545 8.145 6399 Z= 0.281 Chirality : 0.043 0.157 728 Planarity : 0.004 0.036 820 Dihedral : 5.076 20.981 621 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.87 % Allowed : 7.87 % Favored : 91.26 % Rotamer: Outliers : 1.17 % Allowed : 17.97 % 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: -1.41 (0.37), residues: 572 helix: 0.41 (0.43), residues: 173 sheet: -0.83 (0.48), residues: 121 loop : -1.88 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.004 0.001 HIS A 552 PHE 0.009 0.001 PHE A 306 TYR 0.010 0.001 TYR A 75 ARG 0.003 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 66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 495 LYS cc_start: 0.7582 (ptpp) cc_final: 0.7317 (ptmm) REVERT: A 623 ARG cc_start: 0.5447 (OUTLIER) cc_final: 0.4869 (ptt90) REVERT: A 630 ARG cc_start: 0.6942 (tmm-80) cc_final: 0.6617 (ttp80) REVERT: A 699 GLU cc_start: 0.7701 (tt0) cc_final: 0.7406 (tt0) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.6060 time to fit residues: 46.4591 Evaluate side-chains 64 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 187 SER Chi-restraints excluded: chain A residue 246 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: 0.0060 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.193822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.177047 restraints weight = 15708.103| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.89 r_work: 0.4005 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3781 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= 0.220 Angle : 0.578 8.002 6399 Z= 0.301 Chirality : 0.044 0.154 728 Planarity : 0.004 0.037 820 Dihedral : 5.228 23.365 621 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.92 % Favored : 90.21 % Rotamer: Outliers : 2.15 % Allowed : 16.80 % 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: -1.60 (0.36), residues: 572 helix: 0.29 (0.42), residues: 173 sheet: -0.86 (0.49), residues: 119 loop : -2.06 (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 0.014 0.001 PHE A 306 TYR 0.007 0.001 TYR A 75 ARG 0.004 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5472.66 seconds wall clock time: 95 minutes 34.57 seconds (5734.57 seconds total)