Starting phenix.real_space_refine on Fri Aug 22 18:31:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t5s_41060/08_2025/8t5s_41060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t5s_41060/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t5s_41060/08_2025/8t5s_41060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t5s_41060/08_2025/8t5s_41060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t5s_41060/08_2025/8t5s_41060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t5s_41060/08_2025/8t5s_41060.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.75, per 1000 atoms: 0.26 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: 0.49 Conformation dependent library (CDL) restraints added in 331.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.70 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: 1.04 Time building geometry restraints manager: 0.67 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: 1.470 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.640 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- 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 7031 Z= 0.097 Angle : 0.500 9.106 9780 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 : 10.17 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 868 TYR 0.008 0.001 TYR A 911 PHE 0.007 0.001 PHE A 762 TRP 0.017 0.002 TRP A 734 HIS 0.003 0.000 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 7027) covalent geometry : angle 0.49993 ( 9774) hydrogen bonds : bond 0.13946 ( 351) hydrogen bonds : angle 5.16165 ( 972) metal coordination : bond 0.00148 ( 4) metal coordination : angle 0.54081 ( 6) *********************** 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 : 0.178 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: 0.3653 time to fit residues: 27.3534 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 : 0.140 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.099323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073905 restraints weight = 14166.086| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.00 r_work: 0.3099 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7031 Z= 0.198 Angle : 0.584 7.290 9780 Z= 0.294 Chirality : 0.039 0.156 1173 Planarity : 0.004 0.040 1037 Dihedral : 11.250 58.802 1600 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.89 % Allowed : 23.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.33), residues: 685 helix: 2.49 (0.28), residues: 351 sheet: 1.28 (0.65), residues: 73 loop : -0.18 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1011 TYR 0.014 0.001 TYR A 911 PHE 0.012 0.002 PHE A 346 TRP 0.011 0.002 TRP A 863 HIS 0.006 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7027) covalent geometry : angle 0.57869 ( 9774) hydrogen bonds : bond 0.03958 ( 351) hydrogen bonds : angle 4.19693 ( 972) metal coordination : bond 0.00775 ( 4) metal coordination : angle 3.22232 ( 6) *********************** 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 107 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 504 LYS cc_start: 0.8349 (tppt) cc_final: 0.8055 (tppt) REVERT: A 534 MET cc_start: 0.7721 (tpt) cc_final: 0.7415 (tpt) REVERT: A 661 MET cc_start: 0.7779 (tpt) cc_final: 0.7480 (tpp) REVERT: A 735 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8419 (tpt) REVERT: A 897 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 1011 ARG cc_start: 0.8543 (mmp-170) cc_final: 0.8306 (mmp80) outliers start: 37 outliers final: 13 residues processed: 98 average time/residue: 0.3495 time to fit residues: 36.7871 Evaluate side-chains 74 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 436 VAL Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR 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 897 ILE 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 0 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 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 = 0.3654 r_free = 0.3654 target = 0.097576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072537 restraints weight = 14089.380| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.91 r_work: 0.3074 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7031 Z= 0.136 Angle : 0.535 9.161 9780 Z= 0.259 Chirality : 0.037 0.143 1173 Planarity : 0.003 0.038 1037 Dihedral : 11.249 58.530 1598 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.94 % Allowed : 23.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.33), residues: 685 helix: 2.45 (0.27), residues: 351 sheet: 0.59 (0.63), residues: 75 loop : -0.07 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 868 TYR 0.011 0.001 TYR A 911 PHE 0.007 0.001 PHE A 997 TRP 0.009 0.001 TRP A 734 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7027) covalent geometry : angle 0.53242 ( 9774) hydrogen bonds : bond 0.03240 ( 351) hydrogen bonds : angle 4.01671 ( 972) metal coordination : bond 0.00467 ( 4) metal coordination : angle 2.36044 ( 6) *********************** 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 88 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.7713 (tpt) cc_final: 0.7410 (tpt) REVERT: A 544 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: A 863 TRP cc_start: 0.4381 (OUTLIER) cc_final: 0.1780 (p90) REVERT: A 921 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7465 (pp) outliers start: 31 outliers final: 12 residues processed: 77 average time/residue: 0.3801 time to fit residues: 31.4064 Evaluate side-chains 68 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 SER 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 643 LEU Chi-restraints excluded: chain A residue 646 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.096133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.070872 restraints weight = 14212.804| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.90 r_work: 0.3046 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7031 Z= 0.127 Angle : 0.513 7.841 9780 Z= 0.250 Chirality : 0.037 0.148 1173 Planarity : 0.003 0.040 1037 Dihedral : 11.241 58.836 1598 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.25 % Allowed : 23.09 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.33), residues: 685 helix: 2.51 (0.28), residues: 350 sheet: 0.51 (0.59), residues: 80 loop : -0.12 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 868 TYR 0.010 0.001 TYR A 668 PHE 0.007 0.001 PHE A 429 TRP 0.008 0.001 TRP A 734 HIS 0.004 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7027) covalent geometry : angle 0.50971 ( 9774) hydrogen bonds : bond 0.03190 ( 351) hydrogen bonds : angle 3.91533 ( 972) metal coordination : bond 0.00429 ( 4) metal coordination : angle 2.35894 ( 6) *********************** 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 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 477 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6686 (t70) REVERT: A 534 MET cc_start: 0.7696 (tpt) cc_final: 0.7364 (tpt) REVERT: A 543 MET cc_start: 0.8100 (mmt) cc_final: 0.7794 (mmt) REVERT: A 544 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: A 547 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7856 (mm-30) REVERT: A 661 MET cc_start: 0.8205 (tpt) cc_final: 0.7876 (tpt) REVERT: A 667 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8113 (ptp-170) REVERT: A 863 TRP cc_start: 0.4776 (OUTLIER) cc_final: 0.3314 (p90) REVERT: A 921 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7462 (pp) outliers start: 33 outliers final: 11 residues processed: 79 average time/residue: 0.4632 time to fit residues: 38.8527 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 : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 ASP 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.093992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.068777 restraints weight = 14269.964| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.85 r_work: 0.2995 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7031 Z= 0.155 Angle : 0.549 10.349 9780 Z= 0.269 Chirality : 0.037 0.177 1173 Planarity : 0.003 0.030 1037 Dihedral : 11.270 58.710 1598 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.41 % Allowed : 23.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.33), residues: 685 helix: 2.34 (0.27), residues: 351 sheet: 0.31 (0.58), residues: 80 loop : -0.13 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1011 TYR 0.010 0.001 TYR A 911 PHE 0.007 0.001 PHE A 429 TRP 0.008 0.001 TRP A 989 HIS 0.004 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7027) covalent geometry : angle 0.54499 ( 9774) hydrogen bonds : bond 0.03397 ( 351) hydrogen bonds : angle 4.00899 ( 972) metal coordination : bond 0.00603 ( 4) metal coordination : angle 2.76308 ( 6) *********************** 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 81 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 47 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 SER cc_start: 0.8893 (t) cc_final: 0.8545 (t) REVERT: A 534 MET cc_start: 0.7597 (tpt) cc_final: 0.7287 (tpt) REVERT: A 661 MET cc_start: 0.8436 (tpt) cc_final: 0.8069 (tpt) REVERT: A 667 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8200 (ptp-170) REVERT: A 863 TRP cc_start: 0.4717 (OUTLIER) cc_final: 0.3200 (p90) REVERT: A 921 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7635 (pp) outliers start: 34 outliers final: 15 residues processed: 73 average time/residue: 0.4588 time to fit residues: 35.6190 Evaluate side-chains 60 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 528 THR Chi-restraints excluded: chain A residue 544 GLN 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.094038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.068801 restraints weight = 14350.451| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.91 r_work: 0.3003 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7031 Z= 0.130 Angle : 0.523 12.117 9780 Z= 0.257 Chirality : 0.036 0.153 1173 Planarity : 0.003 0.034 1037 Dihedral : 11.274 58.476 1598 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.30 % Allowed : 25.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.33), residues: 685 helix: 2.28 (0.27), residues: 355 sheet: 0.21 (0.58), residues: 80 loop : -0.17 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 865 TYR 0.009 0.001 TYR A 911 PHE 0.007 0.001 PHE A 429 TRP 0.011 0.001 TRP A 989 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7027) covalent geometry : angle 0.52017 ( 9774) hydrogen bonds : bond 0.03227 ( 351) hydrogen bonds : angle 3.93439 ( 972) metal coordination : bond 0.00474 ( 4) metal coordination : angle 2.28589 ( 6) *********************** 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 74 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 472 SER cc_start: 0.8708 (t) cc_final: 0.8366 (t) REVERT: A 534 MET cc_start: 0.7552 (tpt) cc_final: 0.7238 (tpt) REVERT: A 544 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: A 661 MET cc_start: 0.8503 (tpt) cc_final: 0.8116 (tpt) REVERT: A 667 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8208 (ptp-170) REVERT: A 780 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8816 (mm) REVERT: A 863 TRP cc_start: 0.4764 (OUTLIER) cc_final: 0.3049 (p90) REVERT: A 865 ARG cc_start: 0.7710 (mmp-170) cc_final: 0.7261 (mmp-170) REVERT: A 921 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7640 (pp) REVERT: A 1011 ARG cc_start: 0.8850 (mmt180) cc_final: 0.8588 (mmp80) outliers start: 27 outliers final: 10 residues processed: 69 average time/residue: 0.4780 time to fit residues: 35.1557 Evaluate side-chains 55 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 544 GLN 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 775 VAL Chi-restraints excluded: chain A residue 780 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 44 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.095756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.070776 restraints weight = 14089.596| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.82 r_work: 0.3043 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7031 Z= 0.102 Angle : 0.532 10.686 9780 Z= 0.258 Chirality : 0.036 0.155 1173 Planarity : 0.003 0.034 1037 Dihedral : 11.266 58.335 1598 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.34 % Allowed : 25.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.33), residues: 685 helix: 2.46 (0.27), residues: 351 sheet: 0.22 (0.58), residues: 80 loop : -0.06 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 865 TYR 0.010 0.001 TYR A 793 PHE 0.007 0.001 PHE A 997 TRP 0.031 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 7027) covalent geometry : angle 0.53045 ( 9774) hydrogen bonds : bond 0.02937 ( 351) hydrogen bonds : angle 3.80417 ( 972) metal coordination : bond 0.00261 ( 4) metal coordination : angle 1.70595 ( 6) *********************** 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 69 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.7523 (tpt) cc_final: 0.7320 (tpt) REVERT: A 661 MET cc_start: 0.8470 (tpt) cc_final: 0.8053 (tpt) REVERT: A 735 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8414 (tpp) REVERT: A 863 TRP cc_start: 0.4756 (OUTLIER) cc_final: 0.2955 (p90) REVERT: A 921 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7565 (pp) REVERT: A 1011 ARG cc_start: 0.8840 (mmt180) cc_final: 0.8595 (mmp80) outliers start: 21 outliers final: 11 residues processed: 65 average time/residue: 0.4778 time to fit residues: 32.9403 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 : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 735 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 44 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** A 908 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069196 restraints weight = 14264.338| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.90 r_work: 0.3001 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7031 Z= 0.122 Angle : 0.533 10.388 9780 Z= 0.265 Chirality : 0.036 0.191 1173 Planarity : 0.003 0.037 1037 Dihedral : 11.223 58.433 1598 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.50 % Allowed : 25.96 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.33), residues: 685 helix: 2.48 (0.27), residues: 351 sheet: 0.28 (0.58), residues: 80 loop : -0.08 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 865 TYR 0.010 0.001 TYR A 911 PHE 0.007 0.001 PHE A 429 TRP 0.019 0.002 TRP A 734 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7027) covalent geometry : angle 0.53082 ( 9774) hydrogen bonds : bond 0.03155 ( 351) hydrogen bonds : angle 3.86905 ( 972) metal coordination : bond 0.00430 ( 4) metal coordination : angle 2.20954 ( 6) *********************** 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: 22 poor density : 46 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 472 SER cc_start: 0.8600 (t) cc_final: 0.8276 (t) REVERT: A 534 MET cc_start: 0.7585 (tpt) cc_final: 0.7363 (tpt) REVERT: A 661 MET cc_start: 0.8619 (tpt) cc_final: 0.8191 (tpt) REVERT: A 764 ASP cc_start: 0.8589 (m-30) cc_final: 0.8331 (m-30) REVERT: A 780 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8888 (mm) REVERT: A 863 TRP cc_start: 0.4729 (OUTLIER) cc_final: 0.2870 (p90) REVERT: A 921 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7635 (pp) REVERT: A 1011 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8597 (mmp80) outliers start: 22 outliers final: 12 residues processed: 65 average time/residue: 0.4759 time to fit residues: 33.0561 Evaluate side-chains 57 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 775 VAL Chi-restraints excluded: chain A residue 780 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 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 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 15 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.094142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069043 restraints weight = 14429.243| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.89 r_work: 0.3000 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7031 Z= 0.119 Angle : 0.541 8.773 9780 Z= 0.267 Chirality : 0.036 0.180 1173 Planarity : 0.003 0.040 1037 Dihedral : 11.237 58.344 1598 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.66 % Allowed : 25.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.33), residues: 685 helix: 2.46 (0.27), residues: 351 sheet: 0.25 (0.58), residues: 80 loop : -0.03 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 865 TYR 0.010 0.001 TYR A 911 PHE 0.007 0.001 PHE A 429 TRP 0.020 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7027) covalent geometry : angle 0.53865 ( 9774) hydrogen bonds : bond 0.03135 ( 351) hydrogen bonds : angle 3.86829 ( 972) metal coordination : bond 0.00419 ( 4) metal coordination : angle 1.97650 ( 6) *********************** 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 68 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 472 SER cc_start: 0.8628 (t) cc_final: 0.8301 (t) REVERT: A 534 MET cc_start: 0.7576 (tpt) cc_final: 0.7352 (tpt) REVERT: A 735 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8366 (tpt) REVERT: A 863 TRP cc_start: 0.4781 (OUTLIER) cc_final: 0.2807 (p90) REVERT: A 868 ARG cc_start: 0.8306 (mpt-90) cc_final: 0.7802 (pmm150) REVERT: A 921 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7621 (pp) REVERT: A 1011 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8624 (mmp80) outliers start: 23 outliers final: 12 residues processed: 63 average time/residue: 0.4824 time to fit residues: 32.4255 Evaluate side-chains 56 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 735 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 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 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 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.0060 chunk 68 optimal weight: 0.0030 overall best weight: 0.3806 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.095080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070333 restraints weight = 14182.647| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.84 r_work: 0.3030 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7031 Z= 0.109 Angle : 0.573 12.299 9780 Z= 0.273 Chirality : 0.036 0.176 1173 Planarity : 0.003 0.042 1037 Dihedral : 11.230 58.335 1598 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.55 % Allowed : 26.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.33), residues: 685 helix: 2.49 (0.27), residues: 351 sheet: 0.46 (0.58), residues: 78 loop : -0.10 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 865 TYR 0.009 0.001 TYR A 911 PHE 0.006 0.001 PHE A 997 TRP 0.021 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 7027) covalent geometry : angle 0.57112 ( 9774) hydrogen bonds : bond 0.02961 ( 351) hydrogen bonds : angle 3.82005 ( 972) metal coordination : bond 0.00295 ( 4) metal coordination : angle 1.76273 ( 6) ********************** 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: 16 poor density : 47 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.7495 (tpt) cc_final: 0.7291 (tpt) REVERT: A 661 MET cc_start: 0.8556 (tpt) cc_final: 0.8269 (tpt) REVERT: A 735 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8434 (tpt) REVERT: A 863 TRP cc_start: 0.4709 (OUTLIER) cc_final: 0.2462 (p90) REVERT: A 921 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7602 (pp) REVERT: A 1011 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8660 (mmp80) outliers start: 16 outliers final: 11 residues processed: 58 average time/residue: 0.4747 time to fit residues: 29.3372 Evaluate side-chains 58 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 735 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 68 optimal weight: 0.0570 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 875 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.068840 restraints weight = 14338.241| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.89 r_work: 0.3002 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7031 Z= 0.128 Angle : 0.576 10.372 9780 Z= 0.277 Chirality : 0.037 0.197 1173 Planarity : 0.004 0.046 1037 Dihedral : 11.236 58.393 1598 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.03 % Allowed : 25.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.33), residues: 685 helix: 2.36 (0.27), residues: 357 sheet: 0.44 (0.58), residues: 78 loop : -0.01 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 865 TYR 0.010 0.001 TYR A 911 PHE 0.007 0.001 PHE A 429 TRP 0.037 0.002 TRP A 734 HIS 0.003 0.001 HIS A 638 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7027) covalent geometry : angle 0.57407 ( 9774) hydrogen bonds : bond 0.03191 ( 351) hydrogen bonds : angle 3.86932 ( 972) metal coordination : bond 0.00432 ( 4) metal coordination : angle 2.13054 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.38 seconds wall clock time: 31 minutes 10.16 seconds (1870.16 seconds total)