Starting phenix.real_space_refine on Tue Aug 4 21:16:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t5s_41060/08_2026/8t5s_41060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t5s_41060/08_2026/8t5s_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_2026/8t5s_41060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t5s_41060/08_2026/8t5s_41060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t5s_41060/08_2026/8t5s_41060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t5s_41060/08_2026/8t5s_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 1.29, per 1000 atoms: 0.19 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: 0.46 Conformation dependent library (CDL) restraints added in 226.4 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: 0.79 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: 1.13 Time building geometry restraints manager: 0.63 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: 9461 1.82 - 3.64: 283 3.64 - 5.46: 19 5.46 - 7.28: 8 7.28 - 9.11: 3 Bond angle restraints: 9774 Sorted by residual: angle pdb=" O5' A B 30 " pdb=" C5' A B 30 " pdb=" C4' A B 30 " ideal model delta sigma weight residual 109.40 111.90 -2.50 8.00e-01 1.56e+00 9.80e+00 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=" O5' A B 32 " pdb=" C5' A B 32 " pdb=" C4' A B 32 " ideal model delta sigma weight residual 109.40 111.77 -2.37 8.00e-01 1.56e+00 8.77e+00 angle pdb=" O5' U C 29 " pdb=" C5' U C 29 " pdb=" C4' U C 29 " ideal model delta sigma weight residual 109.40 111.75 -2.35 8.00e-01 1.56e+00 8.64e+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: 813 0.029 - 0.059: 179 0.059 - 0.088: 76 0.088 - 0.118: 41 0.118 - 0.147: 64 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=" C2' A B 31 " pdb=" C3' A B 31 " pdb=" O2' A B 31 " pdb=" C1' A B 31 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" C2' A B 32 " pdb=" C3' A B 32 " pdb=" O2' A B 32 " pdb=" C1' A B 32 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.75e-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: 1.580 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.870 Find NCS groups from input model: 0.020 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:8.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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= 0.112 Angle : 0.593 9.106 9780 Z= 0.357 Chirality : 0.046 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 are 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/Z covalent geometry : bond 0.00205 / 0.11 ( 7027) covalent geometry : angle 0.59258 / 0.36 ( 9774) hydrogen bonds : bond 0.13946 / 8.89 ( 351) hydrogen bonds : angle 5.16165 / 3.70 ( 972) metal coordination : bond 0.00148 / 0.07 ( 4) metal coordination : angle 0.54081 / 0.29 ( 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 : 0.144 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: 0.3418 time to fit residues: 25.7842 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 : 0.137 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 506 ASN A 594 ASN A 694 ASN A 908 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.104212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079020 restraints weight = 14491.487| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.22 r_work: 0.3205 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7031 Z= 0.181 Angle : 0.595 6.788 9780 Z= 0.302 Chirality : 0.041 0.167 1173 Planarity : 0.005 0.059 1037 Dihedral : 11.356 69.055 1600 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.57 % Allowed : 24.20 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.33), residues: 685 helix: 2.63 (0.28), residues: 345 sheet: 0.88 (0.64), residues: 75 loop : -0.09 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 868 TYR 0.017 0.002 TYR A 911 PHE 0.020 0.002 PHE A 429 TRP 0.015 0.002 TRP A 863 HIS 0.006 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 7027) covalent geometry : angle 0.58983 / 0.30 ( 9774) hydrogen bonds : bond 0.03946 / 2.58 ( 351) hydrogen bonds : angle 4.23110 / 3.00 ( 972) metal coordination : bond 0.00789 / 0.40 ( 4) metal coordination : angle 3.17516 / 2.08 ( 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 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.231 Fit side-chains REVERT: A 504 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7964 (tppt) REVERT: A 735 MET cc_start: 0.8602 (mmm) cc_final: 0.8330 (tpt) REVERT: A 1011 ARG cc_start: 0.8471 (mmp-170) cc_final: 0.8198 (mmp80) outliers start: 35 outliers final: 15 residues processed: 94 average time/residue: 0.2894 time to fit residues: 29.6649 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 504 LYS 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 756 MET Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 908 ASN Chi-restraints excluded: chain A residue 913 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: 0.0370 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.0570 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 HIS ** A 638 HIS ** 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 = 0.3799 r_free = 0.3799 target = 0.104994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080089 restraints weight = 14005.909| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.82 r_work: 0.3251 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1864 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= 0.112 Angle : 0.521 9.835 9780 Z= 0.255 Chirality : 0.037 0.235 1173 Planarity : 0.003 0.044 1037 Dihedral : 11.194 58.464 1598 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.62 % Allowed : 24.52 % 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 are not related in a simple way. whole: 2.20 (0.33), residues: 685 helix: 2.74 (0.28), residues: 345 sheet: 0.81 (0.64), residues: 75 loop : -0.08 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 852 TYR 0.011 0.001 TYR A 911 PHE 0.007 0.001 PHE A 429 TRP 0.010 0.001 TRP A 863 HIS 0.002 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7027) covalent geometry : angle 0.51852 / 0.25 ( 9774) hydrogen bonds : bond 0.03142 / 2.05 ( 351) hydrogen bonds : angle 4.04851 / 2.88 ( 972) metal coordination : bond 0.00492 / 0.24 ( 4) metal coordination : angle 1.95240 / 1.20 ( 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 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7195 (mtm) REVERT: A 504 LYS cc_start: 0.8257 (tppt) cc_final: 0.8055 (mptt) REVERT: A 735 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8431 (tpt) REVERT: A 863 TRP cc_start: 0.3141 (OUTLIER) cc_final: 0.2009 (p90) REVERT: A 1010 MET cc_start: 0.8311 (ttp) cc_final: 0.8100 (ptp) outliers start: 29 outliers final: 14 residues processed: 86 average time/residue: 0.3764 time to fit residues: 34.5981 Evaluate side-chains 77 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 635 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3709 r_free = 0.3709 target = 0.101192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075877 restraints weight = 14419.355| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.01 r_work: 0.3134 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7031 Z= 0.140 Angle : 0.519 7.764 9780 Z= 0.260 Chirality : 0.037 0.161 1173 Planarity : 0.004 0.045 1037 Dihedral : 11.140 58.632 1598 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.78 % Allowed : 25.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.33), residues: 685 helix: 2.73 (0.28), residues: 344 sheet: 0.65 (0.63), residues: 75 loop : -0.06 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 865 TYR 0.012 0.001 TYR A 911 PHE 0.009 0.001 PHE A 429 TRP 0.010 0.001 TRP A 863 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 7027) covalent geometry : angle 0.51670 / 0.26 ( 9774) hydrogen bonds : bond 0.03253 / 2.14 ( 351) hydrogen bonds : angle 4.02894 / 2.87 ( 972) metal coordination : bond 0.00559 / 0.28 ( 4) metal coordination : angle 1.97184 / 1.22 ( 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 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7205 (mtm) REVERT: A 504 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8000 (tppt) REVERT: A 667 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7955 (ptp-170) REVERT: A 735 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8455 (tpt) REVERT: A 863 TRP cc_start: 0.3564 (OUTLIER) cc_final: 0.2317 (p90) REVERT: A 897 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 948 GLU cc_start: 0.8814 (pm20) cc_final: 0.8602 (pm20) outliers start: 30 outliers final: 13 residues processed: 85 average time/residue: 0.3694 time to fit residues: 33.5293 Evaluate side-chains 80 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 897 ILE 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 72 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 71 optimal weight: 10.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3637 r_free = 0.3637 target = 0.096523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071409 restraints weight = 14286.993| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.88 r_work: 0.3049 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7031 Z= 0.165 Angle : 0.555 9.557 9780 Z= 0.277 Chirality : 0.038 0.163 1173 Planarity : 0.004 0.042 1037 Dihedral : 11.223 58.726 1598 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.57 % Allowed : 24.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.33), residues: 685 helix: 2.43 (0.28), residues: 351 sheet: 0.34 (0.59), residues: 80 loop : -0.14 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 868 TYR 0.013 0.001 TYR A 911 PHE 0.010 0.001 PHE A 346 TRP 0.009 0.001 TRP A 863 HIS 0.006 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 7027) covalent geometry : angle 0.55110 / 0.28 ( 9774) hydrogen bonds : bond 0.03480 / 2.29 ( 351) hydrogen bonds : angle 4.09612 / 2.92 ( 972) metal coordination : bond 0.00695 / 0.34 ( 4) metal coordination : angle 2.71914 / 1.77 ( 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 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7443 (mtm) REVERT: A 472 SER cc_start: 0.8870 (t) cc_final: 0.8520 (t) REVERT: A 477 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6731 (t70) REVERT: A 534 MET cc_start: 0.7608 (tpt) cc_final: 0.7399 (tpt) REVERT: A 543 MET cc_start: 0.8002 (mmt) cc_final: 0.7767 (mmt) REVERT: A 667 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8082 (ptp-170) REVERT: A 752 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8920 (tppp) REVERT: A 863 TRP cc_start: 0.4328 (OUTLIER) cc_final: 0.1808 (p90) REVERT: A 897 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8716 (mp) REVERT: A 921 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7618 (pp) REVERT: A 948 GLU cc_start: 0.8896 (pm20) cc_final: 0.8674 (pm20) REVERT: A 1008 GLN cc_start: 0.7359 (mp10) cc_final: 0.7142 (pm20) REVERT: A 1011 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8115 (mmp80) outliers start: 35 outliers final: 13 residues processed: 80 average time/residue: 0.4083 time to fit residues: 34.6810 Evaluate side-chains 74 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 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 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 752 LYS 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 897 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 53 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3653 r_free = 0.3653 target = 0.097357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072236 restraints weight = 14309.341| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.95 r_work: 0.3071 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7031 Z= 0.109 Angle : 0.527 11.894 9780 Z= 0.259 Chirality : 0.036 0.152 1173 Planarity : 0.003 0.041 1037 Dihedral : 11.268 58.765 1598 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.98 % Allowed : 25.32 % 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 are not related in a simple way. whole: 1.99 (0.33), residues: 685 helix: 2.56 (0.27), residues: 350 sheet: 0.41 (0.62), residues: 75 loop : -0.11 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 865 TYR 0.009 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/Z covalent geometry : bond 0.00231 / 0.11 ( 7027) covalent geometry : angle 0.52495 / 0.26 ( 9774) hydrogen bonds : bond 0.03102 / 2.02 ( 351) hydrogen bonds : angle 3.95544 / 2.83 ( 972) metal coordination : bond 0.00365 / 0.18 ( 4) metal coordination : angle 2.07974 / 1.38 ( 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 82 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7259 (mtm) REVERT: A 472 SER cc_start: 0.8817 (t) cc_final: 0.8479 (t) REVERT: A 477 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6743 (t70) REVERT: A 534 MET cc_start: 0.7619 (tpt) cc_final: 0.7323 (tpt) REVERT: A 661 MET cc_start: 0.8049 (tpt) cc_final: 0.7732 (tpt) REVERT: A 667 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8027 (ptp-170) REVERT: A 863 TRP cc_start: 0.4280 (OUTLIER) cc_final: 0.1965 (p90) REVERT: A 921 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7549 (pp) REVERT: A 948 GLU cc_start: 0.8857 (pm20) cc_final: 0.8575 (pm20) REVERT: A 1011 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8132 (mmp80) outliers start: 25 outliers final: 14 residues processed: 77 average time/residue: 0.4078 time to fit residues: 33.3373 Evaluate side-chains 67 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 477 ASP Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 643 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 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3630 r_free = 0.3630 target = 0.096060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071222 restraints weight = 14131.818| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.89 r_work: 0.3054 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7031 Z= 0.129 Angle : 0.553 12.459 9780 Z= 0.271 Chirality : 0.037 0.159 1173 Planarity : 0.003 0.041 1037 Dihedral : 11.246 59.697 1598 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.46 % Allowed : 25.32 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.33), residues: 685 helix: 2.48 (0.27), residues: 351 sheet: 0.37 (0.58), residues: 80 loop : -0.14 (0.40), residues: 254 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 0.008 0.001 TRP A 863 HIS 0.004 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7027) covalent geometry : angle 0.55016 / 0.27 ( 9774) hydrogen bonds : bond 0.03195 / 2.09 ( 351) hydrogen bonds : angle 3.96440 / 2.83 ( 972) metal coordination : bond 0.00519 / 0.26 ( 4) metal coordination : angle 2.31115 / 1.51 ( 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 80 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7298 (mtm) REVERT: A 472 SER cc_start: 0.8870 (t) cc_final: 0.8533 (t) REVERT: A 477 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6828 (t70) REVERT: A 534 MET cc_start: 0.7601 (tpt) cc_final: 0.7245 (tpt) REVERT: A 661 MET cc_start: 0.8131 (tpt) cc_final: 0.7763 (tpt) REVERT: A 667 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8106 (ptp-170) REVERT: A 863 TRP cc_start: 0.4459 (OUTLIER) cc_final: 0.2277 (p90) REVERT: A 921 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7596 (pp) REVERT: A 948 GLU cc_start: 0.8851 (pm20) cc_final: 0.8575 (pm20) REVERT: A 1011 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8174 (mmp80) outliers start: 28 outliers final: 15 residues processed: 72 average time/residue: 0.3839 time to fit residues: 29.5022 Evaluate side-chains 68 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR 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 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.0070 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3628 r_free = 0.3628 target = 0.095915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071115 restraints weight = 14228.933| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.84 r_work: 0.3055 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7031 Z= 0.123 Angle : 0.551 9.604 9780 Z= 0.269 Chirality : 0.036 0.152 1173 Planarity : 0.003 0.043 1037 Dihedral : 11.265 58.877 1598 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.30 % Allowed : 25.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.33), residues: 685 helix: 2.48 (0.27), residues: 351 sheet: 0.34 (0.58), residues: 80 loop : -0.12 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 865 TYR 0.009 0.001 TYR A 668 PHE 0.007 0.001 PHE A 429 TRP 0.008 0.001 TRP A 863 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7027) covalent geometry : angle 0.54865 / 0.27 ( 9774) hydrogen bonds : bond 0.03111 / 2.04 ( 351) hydrogen bonds : angle 3.94563 / 2.82 ( 972) metal coordination : bond 0.00453 / 0.23 ( 4) metal coordination : angle 2.21813 / 1.46 ( 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 78 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7501 (mtt) REVERT: A 472 SER cc_start: 0.8919 (t) cc_final: 0.8573 (t) REVERT: A 534 MET cc_start: 0.7583 (tpt) cc_final: 0.7270 (tpt) REVERT: A 661 MET cc_start: 0.8197 (tpt) cc_final: 0.7814 (tpt) REVERT: A 667 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8074 (ptp-170) REVERT: A 863 TRP cc_start: 0.4633 (OUTLIER) cc_final: 0.2770 (p90) REVERT: A 921 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7572 (pp) REVERT: A 948 GLU cc_start: 0.8850 (pm20) cc_final: 0.8591 (pm20) outliers start: 27 outliers final: 14 residues processed: 71 average time/residue: 0.3711 time to fit residues: 28.1114 Evaluate side-chains 65 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1011 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** 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 = 0.3611 r_free = 0.3611 target = 0.095031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.069954 restraints weight = 14462.926| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.90 r_work: 0.3020 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3539 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= 0.145 Angle : 0.580 15.271 9780 Z= 0.282 Chirality : 0.037 0.154 1173 Planarity : 0.004 0.051 1037 Dihedral : 11.260 58.911 1598 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.98 % Allowed : 26.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.33), residues: 685 helix: 2.45 (0.27), residues: 351 sheet: 0.18 (0.58), residues: 80 loop : -0.14 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 865 TYR 0.011 0.001 TYR A 911 PHE 0.007 0.001 PHE A 429 TRP 0.018 0.002 TRP A 989 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7027) covalent geometry : angle 0.57737 / 0.28 ( 9774) hydrogen bonds : bond 0.03291 / 2.17 ( 351) hydrogen bonds : angle 3.97960 / 2.85 ( 972) metal coordination : bond 0.00594 / 0.29 ( 4) metal coordination : angle 2.48830 / 1.65 ( 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 73 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7553 (mtt) REVERT: A 472 SER cc_start: 0.8797 (t) cc_final: 0.8464 (t) REVERT: A 534 MET cc_start: 0.7553 (tpt) cc_final: 0.7243 (tpt) REVERT: A 661 MET cc_start: 0.8296 (tpt) cc_final: 0.7953 (tpt) REVERT: A 667 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8101 (ptp-170) REVERT: A 863 TRP cc_start: 0.4775 (OUTLIER) cc_final: 0.3309 (p90) REVERT: A 921 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7666 (pp) REVERT: A 948 GLU cc_start: 0.8867 (pm20) cc_final: 0.8610 (pm20) REVERT: A 1010 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7693 (ttp) REVERT: A 1011 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8394 (mmp80) outliers start: 25 outliers final: 13 residues processed: 67 average time/residue: 0.4447 time to fit residues: 31.6292 Evaluate side-chains 65 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 863 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1010 MET 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: 0.6980 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.095166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070251 restraints weight = 14233.358| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.91 r_work: 0.3024 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7031 Z= 0.124 Angle : 0.559 10.373 9780 Z= 0.274 Chirality : 0.037 0.141 1173 Planarity : 0.003 0.045 1037 Dihedral : 11.287 58.569 1598 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.33), residues: 685 helix: 2.37 (0.27), residues: 351 sheet: 0.16 (0.57), residues: 80 loop : -0.14 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 865 TYR 0.009 0.001 TYR A 668 PHE 0.006 0.001 PHE A 429 TRP 0.011 0.002 TRP A 989 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7027) covalent geometry : angle 0.55631 / 0.27 ( 9774) hydrogen bonds : bond 0.03179 / 2.10 ( 351) hydrogen bonds : angle 3.96039 / 2.83 ( 972) metal coordination : bond 0.00451 / 0.23 ( 4) metal coordination : angle 2.24277 / 1.48 ( 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 69 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 454 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7506 (mtt) REVERT: A 472 SER cc_start: 0.8798 (t) cc_final: 0.8461 (t) REVERT: A 534 MET cc_start: 0.7566 (tpt) cc_final: 0.7285 (tpt) REVERT: A 661 MET cc_start: 0.8360 (tpt) cc_final: 0.8022 (tpt) REVERT: A 667 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8117 (ptp-170) REVERT: A 863 TRP cc_start: 0.4716 (OUTLIER) cc_final: 0.3417 (p90) REVERT: A 921 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7594 (pp) REVERT: A 948 GLU cc_start: 0.8876 (pm20) cc_final: 0.8610 (pm20) REVERT: A 1011 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8397 (mmp80) outliers start: 22 outliers final: 12 residues processed: 64 average time/residue: 0.4015 time to fit residues: 27.2966 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 : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 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: 4.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.093814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068816 restraints weight = 14328.089| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.91 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: 0.8150 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7031 Z= 0.152 Angle : 0.590 15.454 9780 Z= 0.287 Chirality : 0.038 0.173 1173 Planarity : 0.004 0.045 1037 Dihedral : 11.281 58.660 1598 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.50 % Allowed : 26.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.33), residues: 685 helix: 2.31 (0.27), residues: 351 sheet: 0.15 (0.57), residues: 80 loop : -0.19 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 865 TYR 0.012 0.001 TYR A 911 PHE 0.007 0.001 PHE A 429 TRP 0.012 0.002 TRP A 989 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7027) covalent geometry : angle 0.58656 / 0.29 ( 9774) hydrogen bonds : bond 0.03463 / 2.30 ( 351) hydrogen bonds : angle 4.02858 / 2.88 ( 972) metal coordination : bond 0.00633 / 0.31 ( 4) metal coordination : angle 2.64524 / 1.75 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1593.24 seconds wall clock time: 27 minutes 56.11 seconds (1676.11 seconds total)