Starting phenix.real_space_refine on Tue Aug 4 14:49:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q7c_72294/08_2026/9q7c_72294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q7c_72294/08_2026/9q7c_72294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q7c_72294/08_2026/9q7c_72294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q7c_72294/08_2026/9q7c_72294.map" model { file = "/net/cci-nas-00/data/ceres_data/9q7c_72294/08_2026/9q7c_72294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q7c_72294/08_2026/9q7c_72294.cif" } resolution = 4.01 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= 0.008 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2521 2.51 5 N 691 2.21 5 O 791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 4028 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 858 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Time building chain proxies: 0.75, per 1000 atoms: 0.19 Number of scatterers: 4028 At special positions: 0 Unit cell: (69.6, 105.85, 93.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 791 8.00 N 691 7.00 C 2521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 824 " - pdb=" SG CYS A 839 " distance=2.03 Simple disulfide: pdb=" SG CYS A 841 " - pdb=" SG CYS A 853 " distance=2.03 Simple disulfide: pdb=" SG CYS A 859 " - pdb=" SG CYS A 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 866 " - pdb=" SG CYS A 882 " distance=2.03 Simple disulfide: pdb=" SG CYS A 884 " - pdb=" SG CYS A 896 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 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: 0.17 Conformation dependent library (CDL) restraints added in 91.0 milliseconds 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 946 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 14 sheets defined 3.6% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.657A pdb=" N VAL C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.886A pdb=" N ASN D 76 " --> pdb=" O ASN D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.645A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 828 through 829 Processing sheet with id=AA2, first strand: chain 'A' and resid 845 through 847 Processing sheet with id=AA3, first strand: chain 'A' and resid 870 through 872 removed outlier: 3.558A pdb=" N VAL A 883 " --> pdb=" O LYS A 871 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.529A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.368A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 107 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N MET B 34 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.759A pdb=" N ASP C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA C 84 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 67 removed outlier: 3.692A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.826A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.582A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR D 79 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR D 68 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 46 through 50 removed outlier: 6.578A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.562A pdb=" N CYS E 23 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 12 through 13 removed outlier: 6.397A pdb=" N GLU E 105 " --> pdb=" O LEU E 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 49 removed outlier: 3.509A pdb=" N GLN E 37 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) 91 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.24 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: 1303 1.34 - 1.46: 879 1.46 - 1.58: 1898 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 4111 Sorted by residual: bond pdb=" N ILE E 58 " pdb=" CA ILE E 58 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.94e+00 bond pdb=" N LEU E 11 " pdb=" CA LEU E 11 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.02e-02 9.61e+03 8.28e+00 bond pdb=" N VAL A 833 " pdb=" CA VAL A 833 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.62e+00 bond pdb=" N CYS A 830 " pdb=" CA CYS A 830 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.22e-02 6.72e+03 7.57e+00 bond pdb=" N SER A 831 " pdb=" CA SER A 831 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.18e-02 7.18e+03 6.97e+00 ... (remaining 4106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 5318 1.68 - 3.35: 198 3.35 - 5.03: 35 5.03 - 6.70: 9 6.70 - 8.38: 3 Bond angle restraints: 5563 Sorted by residual: angle pdb=" C GLY A 864 " pdb=" N ASN A 865 " pdb=" CA ASN A 865 " ideal model delta sigma weight residual 121.54 129.33 -7.79 1.91e+00 2.74e-01 1.66e+01 angle pdb=" N SER C 9 " pdb=" CA SER C 9 " pdb=" C SER C 9 " ideal model delta sigma weight residual 111.28 107.35 3.93 1.09e+00 8.42e-01 1.30e+01 angle pdb=" CA PRO E 59 " pdb=" C PRO E 59 " pdb=" O PRO E 59 " ideal model delta sigma weight residual 123.16 118.19 4.97 1.49e+00 4.50e-01 1.11e+01 angle pdb=" CA ASN A 834 " pdb=" C ASN A 834 " pdb=" O ASN A 834 " ideal model delta sigma weight residual 122.38 117.43 4.95 1.49e+00 4.50e-01 1.10e+01 angle pdb=" CA ARG E 54 " pdb=" CB ARG E 54 " pdb=" CG ARG E 54 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 ... (remaining 5558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 2220 15.30 - 30.60: 161 30.60 - 45.90: 53 45.90 - 61.20: 21 61.20 - 76.51: 4 Dihedral angle restraints: 2459 sinusoidal: 967 harmonic: 1492 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 152.71 -59.71 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 43.22 49.78 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS A 824 " pdb=" SG CYS A 824 " pdb=" SG CYS A 839 " pdb=" CB CYS A 839 " ideal model delta sinusoidal sigma weight residual -86.00 -42.15 -43.85 1 1.00e+01 1.00e-02 2.68e+01 ... (remaining 2456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 450 0.047 - 0.094: 111 0.094 - 0.140: 38 0.140 - 0.187: 4 0.187 - 0.234: 2 Chirality restraints: 605 Sorted by residual: chirality pdb=" CA VAL A 833 " pdb=" N VAL A 833 " pdb=" C VAL A 833 " pdb=" CB VAL A 833 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE A 832 " pdb=" N ILE A 832 " pdb=" C ILE A 832 " pdb=" CB ILE A 832 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ASN A 865 " pdb=" N ASN A 865 " pdb=" C ASN A 865 " pdb=" CB ASN A 865 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 602 not shown) Planarity restraints: 721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 43 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO E 44 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 44 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 44 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E 94 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO E 95 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 866 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO A 867 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 867 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 867 " -0.023 5.00e-02 4.00e+02 ... (remaining 718 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1882 2.97 - 3.45: 3814 3.45 - 3.93: 6410 3.93 - 4.42: 6891 4.42 - 4.90: 11608 Nonbonded interactions: 30605 Sorted by model distance: nonbonded pdb=" OG SER C 7 " pdb=" OG1 THR C 22 " model vdw 2.487 3.040 nonbonded pdb=" O ALA E 9 " pdb=" OG1 THR E 10 " model vdw 2.497 3.040 nonbonded pdb=" O ASN A 834 " pdb=" N LYS A 836 " model vdw 2.593 3.120 nonbonded pdb=" O ILE A 832 " pdb=" C VAL A 833 " model vdw 2.604 3.270 nonbonded pdb=" O GLY A 864 " pdb=" OD1 ASN A 865 " model vdw 2.606 3.040 ... (remaining 30600 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 group one per residue 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: 3.860 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 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 : 0.004 0.037 4120 Z= 0.231 Angle : 0.773 8.381 5581 Z= 0.429 Chirality : 0.048 0.234 605 Planarity : 0.005 0.056 721 Dihedral : 13.023 76.506 1486 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.47 % Favored : 96.14 % Rotamer: Outliers : 0.23 % Allowed : 0.91 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.24 (0.36), residues: 518 helix: None (None), residues: 0 sheet: -0.22 (0.42), residues: 146 loop : -1.14 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 18 TYR 0.011 0.001 TYR E 49 PHE 0.015 0.002 PHE E 83 TRP 0.021 0.002 TRP D 103 HIS 0.003 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.23 ( 4111) covalent geometry : angle 0.77046 / 0.43 ( 5563) SS BOND : bond 0.00343 / 0.13 ( 9) SS BOND : angle 1.36270 / 0.79 ( 18) hydrogen bonds : bond 0.28664 / 18.25 ( 91) hydrogen bonds : angle 12.54339 / 8.11 ( 222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.6968 (t70) cc_final: 0.6547 (t70) REVERT: B 79 TYR cc_start: 0.6864 (m-80) cc_final: 0.6242 (m-10) REVERT: C 23 CYS cc_start: 0.5994 (t) cc_final: 0.5687 (t) REVERT: D 34 MET cc_start: 0.6204 (mtp) cc_final: 0.5978 (ttp) REVERT: D 43 LYS cc_start: 0.8160 (ptmm) cc_final: 0.7910 (pttp) REVERT: D 47 TRP cc_start: 0.6578 (t60) cc_final: 0.6376 (t60) REVERT: D 78 LEU cc_start: 0.8045 (tp) cc_final: 0.7298 (tp) REVERT: E 82 ASP cc_start: 0.7633 (t0) cc_final: 0.7045 (m-30) REVERT: E 97 THR cc_start: 0.8425 (m) cc_final: 0.8041 (p) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.0679 time to fit residues: 13.8318 Evaluate side-chains 117 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 834 ASN B 3 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.188610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.165983 restraints weight = 7688.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.168821 restraints weight = 5548.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.170404 restraints weight = 4373.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.172020 restraints weight = 3695.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.172878 restraints weight = 3241.562| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4120 Z= 0.174 Angle : 0.677 7.090 5581 Z= 0.355 Chirality : 0.044 0.131 605 Planarity : 0.006 0.065 721 Dihedral : 5.141 17.559 568 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.53 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.25 (0.37), residues: 518 helix: None (None), residues: 0 sheet: -0.23 (0.41), residues: 172 loop : -1.20 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 61 TYR 0.018 0.002 TYR C 49 PHE 0.011 0.003 PHE E 98 TRP 0.018 0.003 TRP B 47 HIS 0.003 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 4111) covalent geometry : angle 0.67352 / 0.35 ( 5563) SS BOND : bond 0.00378 / 0.14 ( 9) SS BOND : angle 1.42737 / 0.78 ( 18) hydrogen bonds : bond 0.03882 / 2.54 ( 91) hydrogen bonds : angle 8.58815 / 5.42 ( 222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 881 GLU cc_start: 0.5924 (mp0) cc_final: 0.5575 (mp0) REVERT: A 889 HIS cc_start: 0.7420 (m90) cc_final: 0.6806 (m90) REVERT: B 57 THR cc_start: 0.7724 (p) cc_final: 0.7479 (p) REVERT: C 49 TYR cc_start: 0.6885 (p90) cc_final: 0.6642 (p90) REVERT: D 34 MET cc_start: 0.7014 (mtp) cc_final: 0.6240 (ttm) REVERT: D 71 ARG cc_start: 0.5085 (tpt170) cc_final: 0.2372 (tpt170) REVERT: D 78 LEU cc_start: 0.8222 (tp) cc_final: 0.7669 (tp) REVERT: D 83 ARG cc_start: 0.6703 (ptp90) cc_final: 0.6503 (ptp-170) REVERT: E 82 ASP cc_start: 0.7830 (t0) cc_final: 0.7146 (m-30) REVERT: E 97 THR cc_start: 0.8339 (m) cc_final: 0.7865 (p) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0834 time to fit residues: 14.3369 Evaluate side-chains 115 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.189002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166048 restraints weight = 7467.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.168762 restraints weight = 5484.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.170456 restraints weight = 4347.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.171996 restraints weight = 3685.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.172814 restraints weight = 3216.680| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4120 Z= 0.137 Angle : 0.626 5.817 5581 Z= 0.327 Chirality : 0.043 0.136 605 Planarity : 0.006 0.072 721 Dihedral : 4.970 18.324 568 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.21 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.30 (0.36), residues: 518 helix: None (None), residues: 0 sheet: -0.19 (0.40), residues: 172 loop : -1.27 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 61 TYR 0.013 0.002 TYR E 49 PHE 0.012 0.002 PHE D 27 TRP 0.019 0.002 TRP D 47 HIS 0.001 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4111) covalent geometry : angle 0.62119 / 0.33 ( 5563) SS BOND : bond 0.00286 / 0.11 ( 9) SS BOND : angle 1.45976 / 0.77 ( 18) hydrogen bonds : bond 0.03542 / 2.41 ( 91) hydrogen bonds : angle 7.83934 / 4.96 ( 222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 871 LYS cc_start: 0.4766 (mmmt) cc_final: 0.4505 (mmmt) REVERT: B 47 TRP cc_start: 0.6994 (t60) cc_final: 0.6671 (t60) REVERT: B 103 TRP cc_start: 0.7861 (m100) cc_final: 0.7482 (m100) REVERT: C 49 TYR cc_start: 0.6868 (p90) cc_final: 0.6608 (p90) REVERT: C 103 LYS cc_start: 0.8359 (tttp) cc_final: 0.7901 (mttm) REVERT: D 34 MET cc_start: 0.6885 (mtp) cc_final: 0.6251 (ttm) REVERT: D 48 VAL cc_start: 0.8562 (t) cc_final: 0.8360 (t) REVERT: D 71 ARG cc_start: 0.4977 (tpt170) cc_final: 0.2286 (tpt170) REVERT: D 78 LEU cc_start: 0.8137 (tp) cc_final: 0.7693 (tp) REVERT: E 82 ASP cc_start: 0.7935 (t0) cc_final: 0.7201 (m-30) REVERT: E 97 THR cc_start: 0.8295 (m) cc_final: 0.7803 (p) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0786 time to fit residues: 13.6255 Evaluate side-chains 119 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 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 = 0.4364 r_free = 0.4364 target = 0.186063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.161956 restraints weight = 7269.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.165138 restraints weight = 5045.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.167253 restraints weight = 3902.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.168750 restraints weight = 3227.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.169585 restraints weight = 2783.832| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4120 Z= 0.164 Angle : 0.643 6.846 5581 Z= 0.337 Chirality : 0.043 0.130 605 Planarity : 0.006 0.072 721 Dihedral : 5.049 18.149 568 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.35 (0.37), residues: 518 helix: None (None), residues: 0 sheet: -0.32 (0.42), residues: 170 loop : -1.25 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.014 0.002 TYR E 49 PHE 0.022 0.002 PHE C 71 TRP 0.030 0.003 TRP B 36 HIS 0.002 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 4111) covalent geometry : angle 0.63747 / 0.34 ( 5563) SS BOND : bond 0.00503 / 0.17 ( 9) SS BOND : angle 1.62177 / 0.87 ( 18) hydrogen bonds : bond 0.03096 / 2.10 ( 91) hydrogen bonds : angle 7.61526 / 4.84 ( 222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 GLU cc_start: 0.7792 (pm20) cc_final: 0.7577 (pm20) REVERT: A 871 LYS cc_start: 0.5263 (mmmt) cc_final: 0.4939 (mmmt) REVERT: A 889 HIS cc_start: 0.7431 (m90) cc_final: 0.6822 (m90) REVERT: B 103 TRP cc_start: 0.7918 (m100) cc_final: 0.7539 (m100) REVERT: C 49 TYR cc_start: 0.7059 (p90) cc_final: 0.6788 (p90) REVERT: C 103 LYS cc_start: 0.8373 (tttp) cc_final: 0.7853 (mttm) REVERT: D 71 ARG cc_start: 0.5267 (tpt170) cc_final: 0.4971 (tpt170) REVERT: E 82 ASP cc_start: 0.7931 (t0) cc_final: 0.7250 (m-30) REVERT: E 97 THR cc_start: 0.8443 (m) cc_final: 0.7927 (p) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0671 time to fit residues: 10.9791 Evaluate side-chains 119 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.186175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.161914 restraints weight = 7273.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.165016 restraints weight = 5213.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.167227 restraints weight = 4049.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.168519 restraints weight = 3366.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.169702 restraints weight = 2947.953| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4120 Z= 0.154 Angle : 0.634 5.733 5581 Z= 0.333 Chirality : 0.042 0.134 605 Planarity : 0.005 0.063 721 Dihedral : 5.027 19.892 568 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.34 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.40 (0.37), residues: 518 helix: None (None), residues: 0 sheet: -0.37 (0.39), residues: 180 loop : -1.29 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.012 0.002 TYR D 91 PHE 0.018 0.002 PHE C 71 TRP 0.018 0.002 TRP B 47 HIS 0.002 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4111) covalent geometry : angle 0.62992 / 0.33 ( 5563) SS BOND : bond 0.00428 / 0.20 ( 9) SS BOND : angle 1.44719 / 0.76 ( 18) hydrogen bonds : bond 0.02896 / 1.97 ( 91) hydrogen bonds : angle 7.34694 / 4.66 ( 222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 863 GLU cc_start: 0.6378 (pm20) cc_final: 0.6140 (pm20) REVERT: A 871 LYS cc_start: 0.5231 (mmmt) cc_final: 0.4969 (mmmt) REVERT: A 889 HIS cc_start: 0.7431 (m90) cc_final: 0.6897 (m90) REVERT: B 79 TYR cc_start: 0.6749 (m-80) cc_final: 0.6462 (m-10) REVERT: B 103 TRP cc_start: 0.7980 (m100) cc_final: 0.7674 (m100) REVERT: C 103 LYS cc_start: 0.8374 (tttp) cc_final: 0.7781 (mttm) REVERT: D 87 THR cc_start: 0.7774 (m) cc_final: 0.7294 (p) REVERT: D 102 TYR cc_start: 0.5937 (m-80) cc_final: 0.5581 (m-10) REVERT: E 56 THR cc_start: 0.8554 (p) cc_final: 0.8342 (p) REVERT: E 82 ASP cc_start: 0.7930 (t0) cc_final: 0.7203 (m-30) REVERT: E 97 THR cc_start: 0.8428 (m) cc_final: 0.7941 (p) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0639 time to fit residues: 10.1967 Evaluate side-chains 117 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 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 = 0.4296 r_free = 0.4296 target = 0.180078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.155599 restraints weight = 7306.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158585 restraints weight = 5153.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160675 restraints weight = 4025.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.162251 restraints weight = 3358.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.163161 restraints weight = 2918.588| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4120 Z= 0.214 Angle : 0.702 5.936 5581 Z= 0.370 Chirality : 0.045 0.133 605 Planarity : 0.006 0.059 721 Dihedral : 5.407 19.486 568 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.46 (0.37), residues: 518 helix: None (None), residues: 0 sheet: -0.57 (0.38), residues: 183 loop : -1.23 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 71 TYR 0.020 0.003 TYR A 855 PHE 0.025 0.003 PHE C 71 TRP 0.032 0.003 TRP D 47 HIS 0.002 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 ( 4111) covalent geometry : angle 0.69739 / 0.37 ( 5563) SS BOND : bond 0.00537 / 0.25 ( 9) SS BOND : angle 1.53737 / 0.80 ( 18) hydrogen bonds : bond 0.03215 / 2.15 ( 91) hydrogen bonds : angle 7.69445 / 4.95 ( 222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 TYR cc_start: 0.6627 (m-80) cc_final: 0.6298 (m-10) REVERT: A 863 GLU cc_start: 0.6442 (pm20) cc_final: 0.6114 (pm20) REVERT: A 871 LYS cc_start: 0.5630 (mmmt) cc_final: 0.5284 (mmmt) REVERT: A 889 HIS cc_start: 0.7487 (m90) cc_final: 0.7002 (m90) REVERT: B 47 TRP cc_start: 0.7777 (t60) cc_final: 0.7473 (t60) REVERT: B 48 VAL cc_start: 0.7614 (t) cc_final: 0.7304 (t) REVERT: B 81 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8418 (tm-30) REVERT: C 103 LYS cc_start: 0.8399 (tttp) cc_final: 0.7886 (mttm) REVERT: D 78 LEU cc_start: 0.8233 (tp) cc_final: 0.7974 (tp) REVERT: D 87 THR cc_start: 0.7860 (m) cc_final: 0.7354 (p) REVERT: D 102 TYR cc_start: 0.6178 (m-80) cc_final: 0.5909 (m-10) REVERT: E 82 ASP cc_start: 0.7995 (t0) cc_final: 0.7255 (m-30) REVERT: E 97 THR cc_start: 0.8531 (m) cc_final: 0.8044 (p) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0654 time to fit residues: 10.4193 Evaluate side-chains 115 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 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 = 0.4300 r_free = 0.4300 target = 0.179705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.155132 restraints weight = 7267.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158404 restraints weight = 5051.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.160726 restraints weight = 3865.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.162330 restraints weight = 3157.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.163300 restraints weight = 2718.186| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4120 Z= 0.203 Angle : 0.695 5.472 5581 Z= 0.366 Chirality : 0.045 0.182 605 Planarity : 0.005 0.056 721 Dihedral : 5.502 19.673 568 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.11 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.50 (0.37), residues: 518 helix: None (None), residues: 0 sheet: -0.67 (0.38), residues: 187 loop : -1.21 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 54 TYR 0.021 0.003 TYR C 49 PHE 0.021 0.003 PHE C 71 TRP 0.023 0.003 TRP D 47 HIS 0.002 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 4111) covalent geometry : angle 0.68914 / 0.36 ( 5563) SS BOND : bond 0.00450 / 0.20 ( 9) SS BOND : angle 1.66863 / 0.87 ( 18) hydrogen bonds : bond 0.03142 / 2.11 ( 91) hydrogen bonds : angle 7.71631 / 5.00 ( 222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 TYR cc_start: 0.6842 (m-80) cc_final: 0.6622 (m-10) REVERT: A 863 GLU cc_start: 0.6616 (pm20) cc_final: 0.6276 (pm20) REVERT: A 871 LYS cc_start: 0.5714 (mmmt) cc_final: 0.5284 (mmmt) REVERT: B 47 TRP cc_start: 0.7659 (t60) cc_final: 0.7292 (t60) REVERT: B 63 VAL cc_start: 0.8660 (t) cc_final: 0.8416 (t) REVERT: B 85 GLU cc_start: 0.8490 (mp0) cc_final: 0.8172 (mp0) REVERT: B 103 TRP cc_start: 0.8052 (m100) cc_final: 0.7764 (m100) REVERT: C 103 LYS cc_start: 0.8454 (tttp) cc_final: 0.7927 (mttm) REVERT: D 71 ARG cc_start: 0.4800 (tpt170) cc_final: 0.3771 (tpp-160) REVERT: D 78 LEU cc_start: 0.8423 (tp) cc_final: 0.8128 (tp) REVERT: D 102 TYR cc_start: 0.5953 (m-80) cc_final: 0.5734 (m-10) REVERT: E 82 ASP cc_start: 0.7959 (t0) cc_final: 0.7245 (m-30) REVERT: E 97 THR cc_start: 0.8635 (m) cc_final: 0.8209 (p) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0708 time to fit residues: 11.8695 Evaluate side-chains 116 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 5 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 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 = 0.4517 r_free = 0.4517 target = 0.199172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183948 restraints weight = 7515.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183948 restraints weight = 6648.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183948 restraints weight = 6648.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183948 restraints weight = 6648.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183948 restraints weight = 6648.469| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4120 Z= 0.136 Angle : 0.657 5.352 5581 Z= 0.343 Chirality : 0.042 0.153 605 Planarity : 0.005 0.055 721 Dihedral : 5.155 19.650 568 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.48 (0.37), residues: 518 helix: None (None), residues: 0 sheet: -0.69 (0.37), residues: 199 loop : -1.18 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 91 TYR 0.020 0.002 TYR B 59 PHE 0.014 0.002 PHE C 71 TRP 0.017 0.002 TRP D 47 HIS 0.005 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4111) covalent geometry : angle 0.65234 / 0.34 ( 5563) SS BOND : bond 0.00347 / 0.15 ( 9) SS BOND : angle 1.49722 / 0.79 ( 18) hydrogen bonds : bond 0.02659 / 1.77 ( 91) hydrogen bonds : angle 7.23610 / 4.70 ( 222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 863 GLU cc_start: 0.6497 (pm20) cc_final: 0.6244 (pm20) REVERT: A 871 LYS cc_start: 0.5652 (mmmt) cc_final: 0.5024 (mmmt) REVERT: B 47 TRP cc_start: 0.7535 (t60) cc_final: 0.7285 (t60) REVERT: B 48 VAL cc_start: 0.7617 (t) cc_final: 0.7351 (t) REVERT: B 57 THR cc_start: 0.7652 (p) cc_final: 0.7401 (p) REVERT: B 103 TRP cc_start: 0.8041 (m100) cc_final: 0.7827 (m100) REVERT: C 103 LYS cc_start: 0.8268 (tttp) cc_final: 0.7860 (mttm) REVERT: D 71 ARG cc_start: 0.4741 (tpt170) cc_final: 0.3860 (tpp-160) REVERT: E 82 ASP cc_start: 0.7954 (t0) cc_final: 0.7223 (m-30) REVERT: E 97 THR cc_start: 0.8523 (m) cc_final: 0.8126 (p) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0714 time to fit residues: 12.1680 Evaluate side-chains 120 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.0070 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** 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 = 0.4525 r_free = 0.4525 target = 0.199239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.183568 restraints weight = 7748.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.183525 restraints weight = 9464.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.184249 restraints weight = 8587.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.184374 restraints weight = 7423.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.184514 restraints weight = 6980.363| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4120 Z= 0.154 Angle : 0.674 5.876 5581 Z= 0.355 Chirality : 0.043 0.154 605 Planarity : 0.005 0.052 721 Dihedral : 5.205 18.333 568 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.27 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.54 (0.37), residues: 518 helix: None (None), residues: 0 sheet: -0.71 (0.37), residues: 192 loop : -1.23 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 38 TYR 0.019 0.002 TYR C 49 PHE 0.015 0.002 PHE C 71 TRP 0.013 0.002 TRP D 47 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 4111) covalent geometry : angle 0.67118 / 0.35 ( 5563) SS BOND : bond 0.00363 / 0.17 ( 9) SS BOND : angle 1.28063 / 0.68 ( 18) hydrogen bonds : bond 0.02778 / 1.81 ( 91) hydrogen bonds : angle 7.24476 / 4.75 ( 222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8651 (mmtm) cc_final: 0.7862 (tptt) REVERT: A 871 LYS cc_start: 0.5796 (mmmt) cc_final: 0.5141 (mmmt) REVERT: B 47 TRP cc_start: 0.7636 (t60) cc_final: 0.7249 (t60) REVERT: B 103 TRP cc_start: 0.8001 (m100) cc_final: 0.7788 (m100) REVERT: C 49 TYR cc_start: 0.7253 (p90) cc_final: 0.7046 (p90) REVERT: C 103 LYS cc_start: 0.8398 (tttp) cc_final: 0.7871 (mttm) REVERT: E 82 ASP cc_start: 0.7824 (t0) cc_final: 0.7229 (m-30) REVERT: E 97 THR cc_start: 0.8404 (m) cc_final: 0.8055 (p) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0748 time to fit residues: 12.6873 Evaluate side-chains 118 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.202655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.187305 restraints weight = 7515.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.188476 restraints weight = 6428.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.188980 restraints weight = 5700.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.188980 restraints weight = 5201.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.189220 restraints weight = 5201.278| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4120 Z= 0.142 Angle : 0.683 6.436 5581 Z= 0.358 Chirality : 0.044 0.175 605 Planarity : 0.005 0.053 721 Dihedral : 5.195 19.699 568 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.61 (0.36), residues: 518 helix: None (None), residues: 0 sheet: -0.88 (0.35), residues: 206 loop : -1.18 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 71 TYR 0.018 0.002 TYR C 49 PHE 0.024 0.002 PHE B 29 TRP 0.037 0.002 TRP D 47 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4111) covalent geometry : angle 0.68144 / 0.36 ( 5563) SS BOND : bond 0.00352 / 0.20 ( 9) SS BOND : angle 1.10637 / 0.59 ( 18) hydrogen bonds : bond 0.02649 / 1.70 ( 91) hydrogen bonds : angle 6.95099 / 4.58 ( 222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8625 (mmtm) cc_final: 0.7821 (tptt) REVERT: B 47 TRP cc_start: 0.7505 (t60) cc_final: 0.7202 (t60) REVERT: B 103 TRP cc_start: 0.8001 (m100) cc_final: 0.7788 (m100) REVERT: C 49 TYR cc_start: 0.7179 (p90) cc_final: 0.6848 (p90) REVERT: C 103 LYS cc_start: 0.8370 (tttp) cc_final: 0.7996 (mttm) REVERT: D 78 LEU cc_start: 0.8056 (tp) cc_final: 0.7843 (tp) REVERT: E 82 ASP cc_start: 0.7867 (t0) cc_final: 0.7224 (m-30) REVERT: E 97 THR cc_start: 0.8382 (m) cc_final: 0.7982 (p) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0777 time to fit residues: 12.5722 Evaluate side-chains 106 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 0.0070 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.201071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.185714 restraints weight = 7754.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.186473 restraints weight = 6641.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.187492 restraints weight = 5862.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.187669 restraints weight = 5338.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.187669 restraints weight = 5054.349| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4120 Z= 0.154 Angle : 0.687 6.379 5581 Z= 0.358 Chirality : 0.043 0.159 605 Planarity : 0.006 0.064 721 Dihedral : 5.265 20.054 568 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.64 (0.36), residues: 518 helix: None (None), residues: 0 sheet: -0.84 (0.36), residues: 201 loop : -1.26 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 38 TYR 0.017 0.002 TYR C 49 PHE 0.014 0.002 PHE C 71 TRP 0.025 0.002 TRP D 47 HIS 0.001 0.000 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 4111) covalent geometry : angle 0.68515 / 0.36 ( 5563) SS BOND : bond 0.00320 / 0.15 ( 9) SS BOND : angle 1.18711 / 0.64 ( 18) hydrogen bonds : bond 0.02622 / 1.70 ( 91) hydrogen bonds : angle 6.96978 / 4.57 ( 222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 941.43 seconds wall clock time: 16 minutes 55.64 seconds (1015.64 seconds total)