Starting phenix.real_space_refine on Tue Mar 11 23:34:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t5s_41060/03_2025/8t5s_41060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t5s_41060/03_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_41060/03_2025/8t5s_41060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t5s_41060/03_2025/8t5s_41060.map" model { file = "/net/cci-nas-00/data/ceres_data/8t5s_41060/03_2025/8t5s_41060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t5s_41060/03_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-5624/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: 6.14, per 1000 atoms: 0.90 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: 1.98 Conformation dependent library (CDL) restraints added in 783.5 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: 2.47 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: 3.17 Time building geometry restraints manager: 2.27 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: 1.500 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.100 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:14.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.810 ------------------------------------------------------------------------------- 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 : 0.675 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: 0.8968 time to fit residues: 67.9233 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 : 0.729 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.104753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079820 restraints weight = 14051.388| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.05 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: 0.7910 moved from start: 0.1694 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 6.150 9774 Z= 0.258 Chirality : 0.037 0.153 1173 Planarity : 0.004 0.043 1037 Dihedral : 11.146 59.200 1600 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.78 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 : 0.707 Fit side-chains revert: symmetry clash REVERT: A 504 LYS cc_start: 0.8221 (tppt) cc_final: 0.8020 (mptt) REVERT: A 534 MET cc_start: 0.7685 (tpt) cc_final: 0.7414 (tpt) REVERT: A 735 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8373 (tpt) REVERT: A 1011 ARG cc_start: 0.8554 (mmp-170) cc_final: 0.8289 (mmp80) outliers start: 32 outliers final: 15 residues processed: 90 average time/residue: 0.8031 time to fit residues: 78.3599 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 : 0.690 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.090477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064852 restraints weight = 14277.748| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.80 r_work: 0.2912 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7027 Z= 0.386 Angle : 0.650 10.432 9774 Z= 0.330 Chirality : 0.042 0.221 1173 Planarity : 0.005 0.039 1037 Dihedral : 11.518 59.001 1598 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.73 % Allowed : 23.89 % 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: 1.39 (0.32), residues: 685 helix: 1.83 (0.27), residues: 357 sheet: 0.46 (0.60), residues: 80 loop : -0.20 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 863 HIS 0.006 0.001 HIS A 406 PHE 0.019 0.002 PHE A 346 TYR 0.017 0.002 TYR A 668 ARG 0.006 0.001 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 89 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7726 (mtt) REVERT: A 472 SER cc_start: 0.9025 (t) cc_final: 0.8653 (t) REVERT: A 534 MET cc_start: 0.7692 (tpt) cc_final: 0.7439 (tpt) REVERT: A 609 ARG cc_start: 0.8715 (ttm170) cc_final: 0.8423 (ttm170) REVERT: A 661 MET cc_start: 0.8502 (tpt) cc_final: 0.8180 (tpt) REVERT: A 863 TRP cc_start: 0.5158 (OUTLIER) cc_final: 0.4772 (p90) REVERT: A 921 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7969 (pp) outliers start: 36 outliers final: 15 residues processed: 81 average time/residue: 1.1264 time to fit residues: 96.7846 Evaluate side-chains 61 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL 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 756 MET Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 884 ASN 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: 0.8980 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 845 GLN A 908 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.092405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.067226 restraints weight = 14328.110| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.83 r_work: 0.2963 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7027 Z= 0.201 Angle : 0.540 9.825 9774 Z= 0.268 Chirality : 0.037 0.147 1173 Planarity : 0.003 0.031 1037 Dihedral : 11.445 58.578 1598 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.62 % Allowed : 24.36 % 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: 1.53 (0.32), residues: 685 helix: 2.08 (0.27), residues: 351 sheet: 0.24 (0.58), residues: 80 loop : -0.20 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.006 0.001 PHE A 997 TYR 0.009 0.001 TYR A 668 ARG 0.003 0.000 ARG A 865 *********************** 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 78 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 49 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7674 (mtt) REVERT: A 472 SER cc_start: 0.8986 (t) cc_final: 0.8611 (t) REVERT: A 534 MET cc_start: 0.7634 (tpt) cc_final: 0.7386 (tpt) REVERT: A 609 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8411 (ttm170) REVERT: A 863 TRP cc_start: 0.4793 (OUTLIER) cc_final: 0.4560 (p90) REVERT: A 1011 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8319 (mmp80) outliers start: 29 outliers final: 10 residues processed: 70 average time/residue: 1.0142 time to fit residues: 75.7986 Evaluate side-chains 51 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 646 LEU 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 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: 0.5980 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.0570 chunk 16 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.093227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068015 restraints weight = 14265.740| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.89 r_work: 0.2983 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4165 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= 0.161 Angle : 0.524 11.647 9774 Z= 0.257 Chirality : 0.037 0.173 1173 Planarity : 0.003 0.034 1037 Dihedral : 11.380 58.377 1598 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.62 % Allowed : 24.20 % 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: 1.63 (0.32), residues: 685 helix: 2.23 (0.27), residues: 350 sheet: 0.12 (0.57), residues: 80 loop : -0.18 (0.40), residues: 255 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 0.008 0.001 PHE A 997 TYR 0.009 0.001 TYR A 911 ARG 0.003 0.000 ARG A1011 *********************** 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 74 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 45 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7574 (mtt) REVERT: A 472 SER cc_start: 0.8955 (t) cc_final: 0.8587 (t) REVERT: A 534 MET cc_start: 0.7599 (tpt) cc_final: 0.7357 (tpt) REVERT: A 609 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8474 (ttm170) REVERT: A 863 TRP cc_start: 0.4676 (OUTLIER) cc_final: 0.4475 (p90) REVERT: A 921 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7712 (pp) REVERT: A 1010 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7625 (ttp) REVERT: A 1011 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8467 (mmp80) outliers start: 29 outliers final: 12 residues processed: 67 average time/residue: 1.1080 time to fit residues: 79.0758 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 : 0.644 ------------------------------------------------------------------------------- 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 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 884 ASN 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 1010 MET 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: 2.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3522 r_free = 0.3522 target = 0.089636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.064502 restraints weight = 14370.415| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.78 r_work: 0.2909 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7027 Z= 0.318 Angle : 0.583 12.099 9774 Z= 0.292 Chirality : 0.039 0.204 1173 Planarity : 0.004 0.031 1037 Dihedral : 11.374 58.961 1598 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.94 % Allowed : 24.20 % 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: 1.44 (0.32), residues: 685 helix: 1.98 (0.27), residues: 357 sheet: -0.08 (0.56), residues: 80 loop : -0.14 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 863 HIS 0.004 0.001 HIS A 406 PHE 0.010 0.002 PHE A 420 TYR 0.012 0.002 TYR A 668 ARG 0.004 0.000 ARG A 852 *********************** 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 77 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 46 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 SER cc_start: 0.8923 (t) cc_final: 0.8589 (t) REVERT: A 534 MET cc_start: 0.7595 (tpt) cc_final: 0.7344 (tpt) REVERT: A 609 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8464 (ttm170) REVERT: A 863 TRP cc_start: 0.5211 (OUTLIER) cc_final: 0.3694 (p90) REVERT: A 868 ARG cc_start: 0.8609 (mtt-85) cc_final: 0.8399 (ptp-170) REVERT: A 921 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8028 (pp) REVERT: A 1010 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7592 (ttp) REVERT: A 1011 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8502 (mmp80) outliers start: 31 outliers final: 17 residues processed: 68 average time/residue: 1.1565 time to fit residues: 83.4363 Evaluate side-chains 62 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 524 CYS 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 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 884 ASN Chi-restraints excluded: chain A residue 904 ILE 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 925 THR Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1010 MET 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: 0.3980 chunk 69 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN ** 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 = 0.3572 r_free = 0.3572 target = 0.092371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067388 restraints weight = 14185.598| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.78 r_work: 0.2970 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4492 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= 0.167 Angle : 0.544 8.536 9774 Z= 0.267 Chirality : 0.037 0.262 1173 Planarity : 0.003 0.030 1037 Dihedral : 11.395 58.382 1598 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.34 % Allowed : 25.96 % Favored : 70.70 % 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 (0.32), residues: 685 helix: 2.21 (0.27), residues: 350 sheet: 0.00 (0.60), residues: 70 loop : -0.13 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 863 HIS 0.003 0.001 HIS A 638 PHE 0.008 0.001 PHE A 420 TYR 0.011 0.001 TYR A 793 ARG 0.004 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 66 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 SER cc_start: 0.8685 (t) cc_final: 0.8361 (t) REVERT: A 534 MET cc_start: 0.7494 (tpt) cc_final: 0.7290 (tpt) REVERT: A 609 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8475 (ttm170) REVERT: A 870 ASP cc_start: 0.9296 (OUTLIER) cc_final: 0.8923 (p0) REVERT: A 921 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7934 (pp) REVERT: A 1011 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8509 (mmp80) outliers start: 21 outliers final: 11 residues processed: 61 average time/residue: 1.1020 time to fit residues: 71.5398 Evaluate side-chains 57 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 CYS 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 748 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 884 ASN 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 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: 3.9990 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3564 r_free = 0.3564 target = 0.091793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066853 restraints weight = 14296.215| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.77 r_work: 0.2961 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7027 Z= 0.183 Angle : 0.547 9.658 9774 Z= 0.268 Chirality : 0.037 0.251 1173 Planarity : 0.003 0.029 1037 Dihedral : 11.344 58.470 1598 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.66 % Allowed : 26.59 % Favored : 69.75 % 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: 1.65 (0.32), residues: 685 helix: 2.16 (0.27), residues: 356 sheet: 0.06 (0.61), residues: 70 loop : -0.07 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 734 HIS 0.003 0.001 HIS A 406 PHE 0.008 0.001 PHE A 429 TYR 0.009 0.001 TYR A 911 ARG 0.007 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 : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 SER cc_start: 0.8742 (t) cc_final: 0.8412 (t) REVERT: A 534 MET cc_start: 0.7552 (tpt) cc_final: 0.7329 (tpt) REVERT: A 543 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.7783 (mmm) REVERT: A 609 ARG cc_start: 0.8793 (ttm170) cc_final: 0.8479 (ttm170) REVERT: A 870 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.8923 (p0) REVERT: A 921 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7893 (pp) REVERT: A 1011 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8555 (mmp80) outliers start: 23 outliers final: 11 residues processed: 62 average time/residue: 1.1163 time to fit residues: 73.7247 Evaluate side-chains 59 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 543 MET 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 870 ASP Chi-restraints excluded: chain A residue 884 ASN 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: 3.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3559 r_free = 0.3559 target = 0.091559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066529 restraints weight = 14333.585| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.83 r_work: 0.2950 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7027 Z= 0.199 Angle : 0.568 10.186 9774 Z= 0.275 Chirality : 0.037 0.251 1173 Planarity : 0.003 0.029 1037 Dihedral : 11.325 58.496 1598 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.50 % Allowed : 26.91 % Favored : 69.59 % 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: 1.65 (0.33), residues: 685 helix: 2.17 (0.27), residues: 356 sheet: 0.26 (0.61), residues: 68 loop : -0.15 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 734 HIS 0.003 0.001 HIS A 406 PHE 0.009 0.001 PHE A 420 TYR 0.010 0.001 TYR A 911 ARG 0.006 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 67 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 LEU cc_start: 0.8551 (mt) cc_final: 0.8275 (tp) REVERT: A 456 ASN cc_start: 0.8738 (m-40) cc_final: 0.8449 (m110) REVERT: A 472 SER cc_start: 0.8608 (t) cc_final: 0.8287 (t) REVERT: A 534 MET cc_start: 0.7552 (tpt) cc_final: 0.7326 (tpt) REVERT: A 543 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.7817 (mmm) REVERT: A 609 ARG cc_start: 0.8803 (ttm170) cc_final: 0.8479 (ttm170) REVERT: A 870 ASP cc_start: 0.9271 (OUTLIER) cc_final: 0.8920 (p0) REVERT: A 921 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7901 (pp) REVERT: A 1011 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8581 (mmp80) outliers start: 22 outliers final: 13 residues processed: 59 average time/residue: 1.0954 time to fit residues: 68.8628 Evaluate side-chains 62 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 543 MET 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 870 ASP Chi-restraints excluded: chain A residue 884 ASN 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: 0.8980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.0060 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.4612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3580 r_free = 0.3580 target = 0.092781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067970 restraints weight = 14473.684| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.87 r_work: 0.2985 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7027 Z= 0.163 Angle : 0.558 11.294 9774 Z= 0.268 Chirality : 0.037 0.258 1173 Planarity : 0.003 0.032 1037 Dihedral : 11.328 58.336 1598 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.39 % Allowed : 27.87 % Favored : 69.75 % 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 (0.32), residues: 685 helix: 2.36 (0.27), residues: 350 sheet: 0.23 (0.60), residues: 68 loop : -0.24 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.008 0.001 PHE A 997 TYR 0.009 0.001 TYR A 911 ARG 0.006 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 63 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 LEU cc_start: 0.8558 (mt) cc_final: 0.8279 (tp) REVERT: A 456 ASN cc_start: 0.8685 (m-40) cc_final: 0.8399 (m110) REVERT: A 472 SER cc_start: 0.8556 (t) cc_final: 0.8240 (t) REVERT: A 534 MET cc_start: 0.7518 (tpt) cc_final: 0.7303 (tpt) REVERT: A 609 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8503 (ttm170) REVERT: A 870 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8861 (p0) REVERT: A 921 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7782 (pp) REVERT: A 1011 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8527 (mmp80) outliers start: 15 outliers final: 11 residues processed: 57 average time/residue: 0.9935 time to fit residues: 60.7175 Evaluate side-chains 60 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 524 CYS 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 815 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 884 ASN 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: 0.8980 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3573 r_free = 0.3573 target = 0.092303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067413 restraints weight = 14370.977| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.85 r_work: 0.2966 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4569 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= 0.179 Angle : 0.578 13.601 9774 Z= 0.275 Chirality : 0.037 0.226 1173 Planarity : 0.003 0.040 1037 Dihedral : 11.306 58.482 1598 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.18 % Allowed : 26.91 % 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: 1.75 (0.33), residues: 685 helix: 2.27 (0.27), residues: 356 sheet: 0.30 (0.61), residues: 68 loop : -0.12 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 PHE 0.007 0.001 PHE A 420 TYR 0.009 0.001 TYR A 911 ARG 0.007 0.000 ARG A 865 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3994.56 seconds wall clock time: 69 minutes 7.30 seconds (4147.30 seconds total)