Starting phenix.real_space_refine on Thu Jan 16 04:03:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0p_39710/01_2025/8z0p_39710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0p_39710/01_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_39710/01_2025/8z0p_39710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0p_39710/01_2025/8z0p_39710.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0p_39710/01_2025/8z0p_39710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0p_39710/01_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-5571/modules/chem_data/mon_lib" Total number of atoms: 9246 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 9239 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 34, 'TRANS': 551} Chain breaks: 6 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' ZN': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.00, 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: 2.51 Conformation dependent library (CDL) restraints added in 592.6 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: 0.81 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: 3.31 Time building geometry restraints manager: 3.01 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.530 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.370 ------------------------------------------------------------------------------- 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 : 0.649 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: 0.4558 time to fit residues: 39.5573 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 : 0.704 ------------------------------------------------------------------------------- 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 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 : 0.707 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: 0.3775 time to fit residues: 34.0808 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 : 0.712 ------------------------------------------------------------------------------- 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 4720 Z= 0.161 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 *********************** 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 : 0.711 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: 0.4208 time to fit residues: 35.6083 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 : 0.742 ------------------------------------------------------------------------------- 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 4720 Z= 0.347 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 *********************** 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 : 0.681 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: 0.4490 time to fit residues: 41.0586 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 : 0.674 ------------------------------------------------------------------------------- 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: 4.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 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: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.197120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.179923 restraints weight = 15633.396| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.95 r_work: 0.4021 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4720 Z= 0.196 Angle : 0.589 9.949 6399 Z= 0.307 Chirality : 0.044 0.154 728 Planarity : 0.004 0.036 820 Dihedral : 5.537 24.773 621 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.22 % Favored : 91.08 % 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: -0.86 (0.47), residues: 117 loop : -1.81 (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 0.015 0.001 PHE A 306 TYR 0.007 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 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 GLU cc_start: 0.7573 (tp30) cc_final: 0.7315 (tp30) REVERT: A 416 MET cc_start: 0.7139 (tmm) cc_final: 0.6931 (ttt) REVERT: A 465 ARG cc_start: 0.5717 (mtm-85) cc_final: 0.5502 (mtm-85) REVERT: A 630 ARG cc_start: 0.7034 (tmm-80) cc_final: 0.6716 (ttp80) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.4448 time to fit residues: 35.5444 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 : 0.832 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.190163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.173122 restraints weight = 15771.879| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.91 r_work: 0.3968 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 4720 Z= 0.367 Angle : 0.706 9.025 6399 Z= 0.376 Chirality : 0.048 0.179 728 Planarity : 0.006 0.051 820 Dihedral : 6.103 25.079 621 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.31 % Favored : 88.81 % Rotamer: Outliers : 3.32 % Allowed : 14.06 % 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: -2.39 (0.34), residues: 572 helix: -0.81 (0.39), residues: 185 sheet: -1.09 (0.47), residues: 121 loop : -2.39 (0.36), residues: 266 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 0.016 0.003 TYR A 329 ARG 0.009 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.6279 (mp10) REVERT: A 246 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7804 (tmmt) REVERT: A 306 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6719 (m-80) REVERT: A 417 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8538 (p) REVERT: A 495 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7429 (ptmm) REVERT: A 623 ARG cc_start: 0.5368 (OUTLIER) cc_final: 0.4686 (ptt90) REVERT: A 630 ARG cc_start: 0.7075 (tmm-80) cc_final: 0.6719 (ttp80) REVERT: A 699 GLU cc_start: 0.7714 (tt0) cc_final: 0.7317 (tt0) outliers start: 17 outliers final: 10 residues processed: 74 average time/residue: 0.4844 time to fit residues: 43.7937 Evaluate side-chains 75 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 348 VAL Chi-restraints excluded: chain A residue 387 THR 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 643 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: 0.5980 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.194218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178347 restraints weight = 15710.435| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.77 r_work: 0.4007 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4720 Z= 0.205 Angle : 0.595 8.469 6399 Z= 0.313 Chirality : 0.044 0.153 728 Planarity : 0.004 0.036 820 Dihedral : 5.661 24.364 621 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.09 % Favored : 90.03 % Rotamer: Outliers : 2.15 % Allowed : 16.41 % Favored : 81.45 % 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: -1.91 (0.36), residues: 572 helix: -0.24 (0.41), residues: 179 sheet: -1.05 (0.48), residues: 119 loop : -2.07 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 659 HIS 0.004 0.001 HIS A 601 PHE 0.016 0.001 PHE A 306 TYR 0.009 0.001 TYR A 75 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.4973 (m-80) REVERT: A 417 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 495 LYS cc_start: 0.7681 (ptpp) cc_final: 0.7347 (ptmm) REVERT: A 623 ARG cc_start: 0.5359 (OUTLIER) cc_final: 0.4728 (ptt90) REVERT: A 630 ARG cc_start: 0.7022 (tmm-80) cc_final: 0.6670 (ttp80) REVERT: A 699 GLU cc_start: 0.7716 (tt0) cc_final: 0.7362 (tt0) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.4552 time to fit residues: 38.3987 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 : 0.713 ------------------------------------------------------------------------------- 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 354 TYR 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: 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: 0.9980 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.191658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175595 restraints weight = 15984.881| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.80 r_work: 0.3978 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 4720 Z= 0.293 Angle : 0.637 8.549 6399 Z= 0.337 Chirality : 0.046 0.161 728 Planarity : 0.005 0.038 820 Dihedral : 5.749 23.651 621 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.97 % Favored : 89.16 % Rotamer: Outliers : 2.93 % Allowed : 16.02 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.35), residues: 572 helix: -0.36 (0.41), residues: 179 sheet: -1.11 (0.48), residues: 119 loop : -2.23 (0.37), residues: 274 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 0.002 PHE A 306 TYR 0.008 0.002 TYR A 480 ARG 0.005 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 76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.6613 (mp10) REVERT: A 176 GLU cc_start: 0.8425 (tp30) cc_final: 0.8205 (tp30) REVERT: A 246 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7820 (tmmt) REVERT: A 417 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8550 (p) REVERT: A 495 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7411 (ptmm) REVERT: A 623 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.4920 (ptt90) REVERT: A 630 ARG cc_start: 0.7001 (tmm-80) cc_final: 0.6658 (ttp80) REVERT: A 643 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6804 (ttt180) REVERT: A 699 GLU cc_start: 0.7785 (tt0) cc_final: 0.7443 (tt0) outliers start: 15 outliers final: 7 residues processed: 69 average time/residue: 0.4735 time to fit residues: 39.9470 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 : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 494 MET 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: 4.9990 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.193644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.177694 restraints weight = 15612.588| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 1.77 r_work: 0.4000 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4720 Z= 0.211 Angle : 0.593 8.194 6399 Z= 0.311 Chirality : 0.044 0.149 728 Planarity : 0.004 0.037 820 Dihedral : 5.556 23.607 621 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.92 % Favored : 90.21 % Rotamer: Outliers : 2.73 % Allowed : 16.41 % 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: -1.87 (0.36), residues: 572 helix: -0.19 (0.41), residues: 179 sheet: -1.05 (0.49), residues: 117 loop : -2.04 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 659 HIS 0.004 0.001 HIS A 601 PHE 0.015 0.001 PHE A 306 TYR 0.009 0.001 TYR A 75 ARG 0.004 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: 14 poor density : 60 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.6943 (mp10) REVERT: A 176 GLU cc_start: 0.8354 (tp30) cc_final: 0.8148 (tp30) REVERT: A 417 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8507 (p) REVERT: A 495 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7348 (ptmm) REVERT: A 623 ARG cc_start: 0.5564 (OUTLIER) cc_final: 0.4934 (ptt90) REVERT: A 630 ARG cc_start: 0.6976 (tmm-80) cc_final: 0.6649 (ttp80) REVERT: A 699 GLU cc_start: 0.7755 (tt0) cc_final: 0.7434 (tt0) outliers start: 14 outliers final: 9 residues processed: 66 average time/residue: 0.4779 time to fit residues: 38.6554 Evaluate side-chains 73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 LEU 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 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: 0.0970 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.196354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.180342 restraints weight = 15856.122| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.79 r_work: 0.4027 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4720 Z= 0.165 Angle : 0.564 8.118 6399 Z= 0.292 Chirality : 0.043 0.146 728 Planarity : 0.004 0.037 820 Dihedral : 5.241 20.581 621 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.09 % Favored : 90.03 % Rotamer: Outliers : 2.34 % Allowed : 16.99 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.36), residues: 572 helix: 0.12 (0.43), residues: 173 sheet: -0.92 (0.49), residues: 119 loop : -2.07 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 659 HIS 0.003 0.001 HIS A 644 PHE 0.012 0.001 PHE A 306 TYR 0.009 0.001 TYR A 75 ARG 0.008 0.000 ARG A 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: A 354 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.4815 (m-80) REVERT: A 417 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8477 (p) REVERT: A 495 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7356 (ptmm) REVERT: A 623 ARG cc_start: 0.5539 (OUTLIER) cc_final: 0.4921 (ptt90) REVERT: A 630 ARG cc_start: 0.6945 (tmm-80) cc_final: 0.6613 (ttp80) REVERT: A 699 GLU cc_start: 0.7721 (tt0) cc_final: 0.7404 (tt0) outliers start: 12 outliers final: 6 residues processed: 67 average time/residue: 0.4687 time to fit residues: 38.8416 Evaluate side-chains 72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.196697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.180759 restraints weight = 15704.340| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.78 r_work: 0.4030 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.029 4720 Z= 0.166 Angle : 0.563 7.988 6399 Z= 0.291 Chirality : 0.043 0.149 728 Planarity : 0.004 0.037 820 Dihedral : 5.135 21.722 621 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.74 % Favored : 90.38 % Rotamer: Outliers : 1.95 % Allowed : 17.19 % 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: -1.60 (0.36), residues: 572 helix: 0.24 (0.43), residues: 173 sheet: -0.88 (0.49), residues: 119 loop : -2.01 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.003 0.001 HIS A 114 PHE 0.011 0.001 PHE A 306 TYR 0.008 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: 5160.87 seconds wall clock time: 91 minutes 25.56 seconds (5485.56 seconds total)