Starting phenix.real_space_refine on Tue Feb 11 23:59:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t5s_41060/02_2025/8t5s_41060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t5s_41060/02_2025/8t5s_41060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t5s_41060/02_2025/8t5s_41060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t5s_41060/02_2025/8t5s_41060.map" model { file = "/net/cci-nas-00/data/ceres_data/8t5s_41060/02_2025/8t5s_41060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t5s_41060/02_2025/8t5s_41060.cif" } resolution = 2.9 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= 0.000 sd= 0.019 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 1 6.06 5 P 62 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 4017 2.51 5 N 1187 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6799 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5510 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 21, 'TRANS': 671} Chain breaks: 3 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 600 Classifications: {'RNA': 30} Modifications used: {'rna3p_pyr': 30} Link IDs: {'rna3p': 29} Chain: "B" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 660 Classifications: {'RNA': 30} Modifications used: {'rna3p_pur': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4622 SG CYS A 891 33.616 20.824 52.033 1.00141.13 S ATOM 4646 SG CYS A 894 33.665 17.107 51.305 1.00141.12 S ATOM 4947 SG CYS A 945 34.617 18.363 54.764 1.00143.31 S ATOM 4992 SG CYS A 950 36.953 18.952 51.820 1.00149.53 S Time building chain proxies: 4.42, per 1000 atoms: 0.65 Number of scatterers: 6799 At special positions: 0 Unit cell: (89.93, 96.278, 105.8, 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 1 29.99 S 40 16.00 P 62 15.00 Mg 1 11.99 O 1491 8.00 N 1187 7.00 C 4017 6.00 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: 1.69 Conformation dependent library (CDL) restraints added in 794.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 894 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 945 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 891 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 950 " Number of angles added : 6 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 5 sheets defined 54.3% alpha, 9.4% beta 30 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.549A pdb=" N VAL A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 339 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.711A pdb=" N VAL A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.743A pdb=" N PHE A 424 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 480 through 495 Processing helix chain 'A' and resid 506 through 514 Processing helix chain 'A' and resid 529 through 557 Processing helix chain 'A' and resid 589 through 605 removed outlier: 4.248A pdb=" N GLN A 593 " --> pdb=" O HIS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.902A pdb=" N ARG A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 654 removed outlier: 3.991A pdb=" N ALA A 642 " --> pdb=" O HIS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'A' and resid 658 through 676 removed outlier: 3.846A pdb=" N GLY A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 697 Processing helix chain 'A' and resid 708 through 721 Processing helix chain 'A' and resid 722 through 728 removed outlier: 4.175A pdb=" N LEU A 728 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 764 Processing helix chain 'A' and resid 773 through 778 removed outlier: 3.526A pdb=" N GLU A 778 " --> pdb=" O VAL A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 Processing helix chain 'A' and resid 820 through 847 removed outlier: 3.614A pdb=" N ARG A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 859 Processing helix chain 'A' and resid 861 through 881 removed outlier: 3.558A pdb=" N ILE A 866 " --> pdb=" O ILE A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 4.218A pdb=" N TRP A 919 " --> pdb=" O PRO A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 996 removed outlier: 3.873A pdb=" N ILE A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1014 removed outlier: 3.653A pdb=" N THR A1009 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A1014 " --> pdb=" O MET A1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 374 removed outlier: 3.657A pdb=" N GLN A 372 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA A 344 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA A 394 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE A 346 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 347 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 310 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 311 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 519 through 523 removed outlier: 3.747A pdb=" N VAL A 771 " --> pdb=" O GLU A 733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AA4, first strand: chain 'A' and resid 911 through 913 removed outlier: 4.204A pdb=" N THR A1000 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 943 through 944 removed outlier: 3.736A pdb=" N GLY A 955 " --> pdb=" O ILE A 943 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2040 1.34 - 1.46: 1372 1.46 - 1.58: 3434 1.58 - 1.70: 121 1.70 - 1.81: 60 Bond restraints: 7027 Sorted by residual: bond pdb=" C TRP A 863 " pdb=" N PRO A 864 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.55e+00 bond pdb=" C4 ADP A1103 " pdb=" C5 ADP A1103 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" CA ASN A 884 " pdb=" CB ASN A 884 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.56e-02 4.11e+03 1.18e+00 bond pdb=" CB ASN A 884 " pdb=" CG ASN A 884 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CB GLU A 948 " pdb=" CG GLU A 948 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.28e-01 ... (remaining 7022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 9641 1.82 - 3.64: 103 3.64 - 5.46: 19 5.46 - 7.28: 8 7.28 - 9.11: 3 Bond angle restraints: 9774 Sorted by residual: angle pdb=" CB MET A 650 " pdb=" CG MET A 650 " pdb=" SD MET A 650 " ideal model delta sigma weight residual 112.70 121.81 -9.11 3.00e+00 1.11e-01 9.21e+00 angle pdb=" C ARG A 883 " pdb=" N ASN A 884 " pdb=" CA ASN A 884 " ideal model delta sigma weight residual 123.05 127.75 -4.70 1.57e+00 4.06e-01 8.96e+00 angle pdb=" CA ARG A 865 " pdb=" CB ARG A 865 " pdb=" CG ARG A 865 " ideal model delta sigma weight residual 114.10 119.68 -5.58 2.00e+00 2.50e-01 7.78e+00 angle pdb=" CB ARG A 865 " pdb=" CG ARG A 865 " pdb=" CD ARG A 865 " ideal model delta sigma weight residual 111.30 117.55 -6.25 2.30e+00 1.89e-01 7.37e+00 angle pdb=" CB MET A 445 " pdb=" CG MET A 445 " pdb=" SD MET A 445 " ideal model delta sigma weight residual 112.70 120.79 -8.09 3.00e+00 1.11e-01 7.27e+00 ... (remaining 9769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 3849 21.41 - 42.82: 360 42.82 - 64.23: 83 64.23 - 85.64: 7 85.64 - 107.05: 4 Dihedral angle restraints: 4303 sinusoidal: 2272 harmonic: 2031 Sorted by residual: dihedral pdb=" O2A ADP A1103 " pdb=" O3A ADP A1103 " pdb=" PA ADP A1103 " pdb=" PB ADP A1103 " ideal model delta sinusoidal sigma weight residual -60.00 -167.05 107.05 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O1B ADP A1103 " pdb=" O3A ADP A1103 " pdb=" PB ADP A1103 " pdb=" PA ADP A1103 " ideal model delta sinusoidal sigma weight residual -60.00 8.24 -68.24 1 2.00e+01 2.50e-03 1.51e+01 dihedral pdb=" C4' ADP A1103 " pdb=" C5' ADP A1103 " pdb=" O5' ADP A1103 " pdb=" PA ADP A1103 " ideal model delta sinusoidal sigma weight residual 180.00 114.28 65.72 1 2.00e+01 2.50e-03 1.41e+01 ... (remaining 4300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 877 0.029 - 0.059: 175 0.059 - 0.088: 76 0.088 - 0.118: 41 0.118 - 0.147: 4 Chirality restraints: 1173 Sorted by residual: chirality pdb=" CA ASN A 884 " pdb=" N ASN A 884 " pdb=" C ASN A 884 " pdb=" CB ASN A 884 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CB THR A 552 " pdb=" CA THR A 552 " pdb=" OG1 THR A 552 " pdb=" CG2 THR A 552 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA TRP A 863 " pdb=" N TRP A 863 " pdb=" C TRP A 863 " pdb=" CB TRP A 863 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1170 not shown) Planarity restraints: 1037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 863 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 864 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 883 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.20e+00 pdb=" C ARG A 883 " -0.019 2.00e-02 2.50e+03 pdb=" O ARG A 883 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN A 884 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 638 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 639 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " -0.014 5.00e-02 4.00e+02 ... (remaining 1034 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 768 2.75 - 3.29: 6519 3.29 - 3.82: 12585 3.82 - 4.36: 13656 4.36 - 4.90: 21943 Nonbonded interactions: 55471 Sorted by model distance: nonbonded pdb=" ND2 ASN A 908 " pdb=" O2' A B 36 " model vdw 2.212 3.120 nonbonded pdb=" N GLU A 948 " pdb=" OE1 GLU A 948 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR A 742 " pdb=" OP2 A B 30 " model vdw 2.247 3.040 nonbonded pdb="MG MG A1102 " pdb=" O3B ADP A1103 " model vdw 2.299 2.170 nonbonded pdb=" N GLU A 778 " pdb=" OE1 GLU A 778 " model vdw 2.314 3.120 ... (remaining 55466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.920 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.510 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.002 0.029 7027 Z= 0.122 Angle : 0.500 9.106 9774 Z= 0.242 Chirality : 0.034 0.147 1173 Planarity : 0.003 0.044 1037 Dihedral : 16.224 107.051 2981 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.80 % Allowed : 30.73 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.33), residues: 685 helix: 2.94 (0.27), residues: 340 sheet: 0.96 (0.65), residues: 75 loop : 0.08 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 734 HIS 0.003 0.000 HIS A 638 PHE 0.007 0.001 PHE A 762 TYR 0.008 0.001 TYR A 911 ARG 0.004 0.000 ARG A 868 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.667 Fit side-chains REVERT: A 702 THR cc_start: 0.8298 (m) cc_final: 0.8024 (p) REVERT: A 893 LYS cc_start: 0.8175 (tttt) cc_final: 0.7956 (mtpt) REVERT: A 1010 MET cc_start: 0.7787 (ttm) cc_final: 0.7102 (ttp) outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 0.8763 time to fit residues: 66.2385 Evaluate side-chains 61 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 992 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 506 ASN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN A 908 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.104765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079813 restraints weight = 14050.106| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.06 r_work: 0.3212 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7027 Z= 0.202 Angle : 0.518 6.149 9774 Z= 0.258 Chirality : 0.037 0.153 1173 Planarity : 0.004 0.043 1037 Dihedral : 11.146 59.220 1600 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.10 % Allowed : 24.04 % Favored : 70.86 % 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: 2.38 (0.33), residues: 685 helix: 2.85 (0.28), residues: 346 sheet: 1.08 (0.64), residues: 75 loop : -0.01 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 863 HIS 0.004 0.001 HIS A 449 PHE 0.011 0.001 PHE A 762 TYR 0.012 0.001 TYR A 911 ARG 0.007 0.000 ARG A 868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 504 LYS cc_start: 0.8219 (tppt) cc_final: 0.8018 (mptt) REVERT: A 534 MET cc_start: 0.7684 (tpt) cc_final: 0.7413 (tpt) REVERT: A 735 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8372 (tpt) REVERT: A 1011 ARG cc_start: 0.8555 (mmp-170) cc_final: 0.8289 (mmp80) outliers start: 32 outliers final: 15 residues processed: 90 average time/residue: 0.8364 time to fit residues: 81.3245 Evaluate side-chains 78 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 868 ARG Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.070678 restraints weight = 14210.661| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.90 r_work: 0.3034 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7027 Z= 0.231 Angle : 0.544 8.442 9774 Z= 0.270 Chirality : 0.038 0.140 1173 Planarity : 0.003 0.039 1037 Dihedral : 11.238 58.705 1598 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.41 % Allowed : 24.20 % Favored : 70.38 % 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: 1.89 (0.33), residues: 685 helix: 2.38 (0.27), residues: 350 sheet: 0.72 (0.60), residues: 80 loop : -0.14 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 989 HIS 0.005 0.001 HIS A 406 PHE 0.012 0.001 PHE A 346 TYR 0.013 0.001 TYR A 911 ARG 0.006 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7458 (mtm) REVERT: A 472 SER cc_start: 0.8873 (t) cc_final: 0.8515 (t) REVERT: A 534 MET cc_start: 0.7750 (tpt) cc_final: 0.7443 (tpt) REVERT: A 543 MET cc_start: 0.7944 (mmt) cc_final: 0.7599 (mmt) REVERT: A 544 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: A 609 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8359 (ttm170) REVERT: A 735 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8434 (tpt) REVERT: A 837 MET cc_start: 0.8656 (tpp) cc_final: 0.8450 (tpp) REVERT: A 863 TRP cc_start: 0.4556 (OUTLIER) cc_final: 0.2994 (p90) REVERT: A 921 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7434 (pp) outliers start: 34 outliers final: 14 residues processed: 86 average time/residue: 1.1592 time to fit residues: 106.1273 Evaluate side-chains 65 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.068627 restraints weight = 14305.879| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.87 r_work: 0.2996 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7027 Z= 0.234 Angle : 0.545 10.192 9774 Z= 0.268 Chirality : 0.038 0.151 1173 Planarity : 0.004 0.039 1037 Dihedral : 11.287 59.768 1598 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.73 % Allowed : 23.09 % Favored : 71.18 % 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: 1.80 (0.33), residues: 685 helix: 2.32 (0.28), residues: 351 sheet: 0.39 (0.59), residues: 80 loop : -0.11 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 863 HIS 0.003 0.001 HIS A 449 PHE 0.008 0.001 PHE A 429 TYR 0.011 0.001 TYR A 668 ARG 0.003 0.000 ARG A1011 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 50 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7517 (mtt) REVERT: A 472 SER cc_start: 0.8969 (t) cc_final: 0.8618 (t) REVERT: A 534 MET cc_start: 0.7620 (tpt) cc_final: 0.7307 (tpt) REVERT: A 543 MET cc_start: 0.8066 (mmt) cc_final: 0.7817 (mmt) REVERT: A 544 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: A 547 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 609 ARG cc_start: 0.8638 (ttm170) cc_final: 0.8356 (ttm170) REVERT: A 661 MET cc_start: 0.8372 (tpt) cc_final: 0.7991 (tpt) REVERT: A 863 TRP cc_start: 0.4885 (OUTLIER) cc_final: 0.3661 (p90) REVERT: A 865 ARG cc_start: 0.7532 (mmp-170) cc_final: 0.7201 (mmp-170) REVERT: A 1011 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8388 (mmp80) outliers start: 36 outliers final: 12 residues processed: 73 average time/residue: 1.0600 time to fit residues: 82.5180 Evaluate side-chains 61 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 66 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.094623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.069599 restraints weight = 14214.767| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.83 r_work: 0.3012 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7027 Z= 0.172 Angle : 0.525 11.188 9774 Z= 0.256 Chirality : 0.037 0.176 1173 Planarity : 0.003 0.033 1037 Dihedral : 11.294 58.449 1598 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.10 % Allowed : 23.57 % Favored : 71.34 % 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: 1.74 (0.33), residues: 685 helix: 2.26 (0.27), residues: 355 sheet: 0.33 (0.58), residues: 80 loop : -0.16 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.007 0.001 PHE A 429 TYR 0.010 0.001 TYR A 911 ARG 0.007 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7481 (mtt) REVERT: A 472 SER cc_start: 0.8884 (t) cc_final: 0.8535 (t) REVERT: A 504 LYS cc_start: 0.8491 (tppt) cc_final: 0.8273 (tppt) REVERT: A 534 MET cc_start: 0.7600 (tpt) cc_final: 0.7293 (tpt) REVERT: A 543 MET cc_start: 0.8117 (mmt) cc_final: 0.7809 (mmt) REVERT: A 544 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: A 547 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 609 ARG cc_start: 0.8646 (ttm170) cc_final: 0.8367 (ttm170) REVERT: A 661 MET cc_start: 0.8419 (tpt) cc_final: 0.8042 (tpt) REVERT: A 863 TRP cc_start: 0.4606 (OUTLIER) cc_final: 0.2588 (p90) REVERT: A 921 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7631 (pp) REVERT: A 1011 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8500 (mmp80) outliers start: 32 outliers final: 13 residues processed: 80 average time/residue: 1.1540 time to fit residues: 98.1438 Evaluate side-chains 67 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.092727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.067605 restraints weight = 14181.562| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.82 r_work: 0.2974 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7027 Z= 0.224 Angle : 0.551 11.204 9774 Z= 0.273 Chirality : 0.038 0.161 1173 Planarity : 0.004 0.049 1037 Dihedral : 11.283 58.654 1598 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.78 % Allowed : 24.20 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.33), residues: 685 helix: 2.21 (0.27), residues: 355 sheet: 0.27 (0.59), residues: 80 loop : -0.15 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 989 HIS 0.003 0.001 HIS A 638 PHE 0.007 0.001 PHE A 429 TYR 0.011 0.001 TYR A 668 ARG 0.005 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 46 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7592 (mtt) REVERT: A 472 SER cc_start: 0.8912 (t) cc_final: 0.8566 (t) REVERT: A 534 MET cc_start: 0.7575 (tpt) cc_final: 0.7267 (tpt) REVERT: A 544 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: A 609 ARG cc_start: 0.8713 (ttm170) cc_final: 0.8425 (ttm170) REVERT: A 863 TRP cc_start: 0.4907 (OUTLIER) cc_final: 0.2704 (p90) REVERT: A 921 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7753 (pp) REVERT: A 1011 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8531 (mmp80) outliers start: 30 outliers final: 15 residues processed: 71 average time/residue: 1.1712 time to fit residues: 88.1578 Evaluate side-chains 61 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 39 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068576 restraints weight = 14166.002| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.86 r_work: 0.2996 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7027 Z= 0.168 Angle : 0.553 11.006 9774 Z= 0.271 Chirality : 0.037 0.232 1173 Planarity : 0.003 0.031 1037 Dihedral : 11.301 58.431 1598 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.98 % Allowed : 25.16 % Favored : 70.86 % 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: 1.72 (0.33), residues: 685 helix: 2.26 (0.27), residues: 355 sheet: 0.26 (0.58), residues: 80 loop : -0.16 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.007 0.001 PHE A 762 TYR 0.010 0.001 TYR A 911 ARG 0.007 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7497 (mtt) REVERT: A 472 SER cc_start: 0.8719 (t) cc_final: 0.8389 (t) REVERT: A 534 MET cc_start: 0.7544 (tpt) cc_final: 0.7231 (tpt) REVERT: A 609 ARG cc_start: 0.8774 (ttm170) cc_final: 0.8503 (ttm170) REVERT: A 764 ASP cc_start: 0.8572 (m-30) cc_final: 0.8315 (m-30) REVERT: A 863 TRP cc_start: 0.4845 (OUTLIER) cc_final: 0.2806 (p90) REVERT: A 921 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7714 (pp) REVERT: A 1011 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8560 (mmp80) outliers start: 25 outliers final: 13 residues processed: 66 average time/residue: 1.1030 time to fit residues: 77.4744 Evaluate side-chains 59 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.0470 chunk 41 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068002 restraints weight = 14234.016| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.81 r_work: 0.2984 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7027 Z= 0.185 Angle : 0.549 8.973 9774 Z= 0.271 Chirality : 0.038 0.293 1173 Planarity : 0.003 0.031 1037 Dihedral : 11.278 58.484 1598 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.66 % Allowed : 26.43 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.33), residues: 685 helix: 2.34 (0.27), residues: 351 sheet: 0.24 (0.58), residues: 80 loop : -0.09 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.007 0.001 PHE A 429 TYR 0.012 0.001 TYR A 793 ARG 0.008 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7649 (mtt) REVERT: A 472 SER cc_start: 0.8845 (t) cc_final: 0.8498 (t) REVERT: A 534 MET cc_start: 0.7487 (tpt) cc_final: 0.7274 (tpt) REVERT: A 609 ARG cc_start: 0.8759 (ttm170) cc_final: 0.8492 (ttm170) REVERT: A 661 MET cc_start: 0.8585 (tpt) cc_final: 0.8306 (tpt) REVERT: A 759 LEU cc_start: 0.9086 (mt) cc_final: 0.8812 (mp) REVERT: A 764 ASP cc_start: 0.8583 (m-30) cc_final: 0.8334 (m-30) REVERT: A 863 TRP cc_start: 0.5015 (OUTLIER) cc_final: 0.2567 (p90) REVERT: A 921 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7764 (pp) REVERT: A 1011 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8584 (mmp80) outliers start: 23 outliers final: 12 residues processed: 63 average time/residue: 1.1324 time to fit residues: 76.0172 Evaluate side-chains 60 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 39 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.094422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.069428 restraints weight = 14253.131| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.92 r_work: 0.3010 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7027 Z= 0.154 Angle : 0.566 13.768 9774 Z= 0.273 Chirality : 0.038 0.331 1173 Planarity : 0.003 0.029 1037 Dihedral : 11.273 58.307 1598 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.55 % Allowed : 27.23 % Favored : 70.22 % 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: 1.89 (0.33), residues: 685 helix: 2.40 (0.27), residues: 351 sheet: 0.39 (0.63), residues: 70 loop : -0.05 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.007 0.001 PHE A 997 TYR 0.010 0.001 TYR A 911 ARG 0.009 0.000 ARG A 865 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.7800 (mmm) cc_final: 0.7540 (mtt) REVERT: A 472 SER cc_start: 0.8587 (t) cc_final: 0.8258 (t) REVERT: A 534 MET cc_start: 0.7532 (tpt) cc_final: 0.7327 (tpt) REVERT: A 609 ARG cc_start: 0.8751 (ttm170) cc_final: 0.8481 (ttm170) REVERT: A 764 ASP cc_start: 0.8574 (m-30) cc_final: 0.8323 (m-30) REVERT: A 863 TRP cc_start: 0.5023 (OUTLIER) cc_final: 0.2561 (p90) REVERT: A 870 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8915 (p0) REVERT: A 921 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7625 (pp) REVERT: A 1011 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8553 (mmp80) outliers start: 16 outliers final: 11 residues processed: 60 average time/residue: 1.1913 time to fit residues: 76.1572 Evaluate side-chains 60 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.0030 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069379 restraints weight = 14406.964| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.89 r_work: 0.3012 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7027 Z= 0.156 Angle : 0.568 13.509 9774 Z= 0.275 Chirality : 0.037 0.190 1173 Planarity : 0.003 0.030 1037 Dihedral : 11.256 58.327 1598 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.87 % Allowed : 26.75 % Favored : 70.38 % 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: 1.84 (0.33), residues: 685 helix: 2.40 (0.27), residues: 351 sheet: 0.49 (0.58), residues: 78 loop : -0.20 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.006 0.001 PHE A 997 TYR 0.010 0.001 TYR A 911 ARG 0.007 0.000 ARG A 865 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1370 Ramachandran restraints generated. 685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7794 (mmm) cc_final: 0.7535 (mtt) REVERT: A 472 SER cc_start: 0.8569 (t) cc_final: 0.8260 (t) REVERT: A 534 MET cc_start: 0.7532 (tpt) cc_final: 0.7325 (tpt) REVERT: A 609 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8493 (ttm170) REVERT: A 764 ASP cc_start: 0.8547 (m-30) cc_final: 0.8294 (m-30) REVERT: A 863 TRP cc_start: 0.4947 (OUTLIER) cc_final: 0.2428 (p90) REVERT: A 921 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7601 (pp) REVERT: A 1011 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8575 (mmp80) outliers start: 18 outliers final: 13 residues processed: 66 average time/residue: 1.1388 time to fit residues: 79.8853 Evaluate side-chains 60 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.092459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.067390 restraints weight = 14347.792| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.81 r_work: 0.2971 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7027 Z= 0.220 Angle : 0.586 10.753 9774 Z= 0.288 Chirality : 0.037 0.178 1173 Planarity : 0.004 0.035 1037 Dihedral : 11.258 58.526 1598 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.34 % Allowed : 26.43 % Favored : 70.22 % 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: 1.77 (0.33), residues: 685 helix: 2.24 (0.27), residues: 357 sheet: 0.41 (0.59), residues: 78 loop : -0.10 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.008 0.001 PHE A 429 TYR 0.017 0.001 TYR A 793 ARG 0.008 0.000 ARG A 868 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3870.65 seconds wall clock time: 69 minutes 25.44 seconds (4165.44 seconds total)