Starting phenix.real_space_refine on Fri Aug 22 18:06:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t07_40937/08_2025/8t07_40937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t07_40937/08_2025/8t07_40937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t07_40937/08_2025/8t07_40937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t07_40937/08_2025/8t07_40937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t07_40937/08_2025/8t07_40937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t07_40937/08_2025/8t07_40937.map" } resolution = 3.38 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= 0.003 sd= 0.066 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 44 5.16 5 C 4352 2.51 5 N 1090 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6710 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.24 Number of scatterers: 6710 At special positions: 0 Unit cell: (87.15, 110.39, 104.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 44 16.00 O 1222 8.00 N 1090 7.00 C 4352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.04 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 259.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 44.0% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.586A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 30 through 50 Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.701A pdb=" N CYS A 59 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.620A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 115 through 141 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.513A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 30 through 50 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.702A pdb=" N CYS B 59 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 87 removed outlier: 3.620A pdb=" N LEU B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 115 through 141 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 177 through 195 removed outlier: 3.513A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'F' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.952A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.710A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.952A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.709A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N HIS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1014 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: 0.69 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1243 1.33 - 1.46: 1814 1.46 - 1.58: 3759 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 6888 Sorted by residual: bond pdb=" C ARG B 93 " pdb=" N SER B 94 " ideal model delta sigma weight residual 1.335 1.423 -0.088 1.30e-02 5.92e+03 4.61e+01 bond pdb=" N ARG C 68 " pdb=" CA ARG C 68 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" N ARG E 68 " pdb=" CA ARG E 68 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" C ALA B 86 " pdb=" N ASP B 87 " ideal model delta sigma weight residual 1.330 1.277 0.053 1.30e-02 5.92e+03 1.69e+01 bond pdb=" N SER D 7 " pdb=" CA SER D 7 " ideal model delta sigma weight residual 1.463 1.488 -0.025 6.90e-03 2.10e+04 1.34e+01 ... (remaining 6883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 5911 1.53 - 3.06: 2675 3.06 - 4.58: 679 4.58 - 6.11: 66 6.11 - 7.64: 7 Bond angle restraints: 9338 Sorted by residual: angle pdb=" CA GLY D 66 " pdb=" C GLY D 66 " pdb=" O GLY D 66 " ideal model delta sigma weight residual 122.23 118.61 3.62 6.90e-01 2.10e+00 2.76e+01 angle pdb=" CA GLY F 66 " pdb=" C GLY F 66 " pdb=" O GLY F 66 " ideal model delta sigma weight residual 122.23 118.65 3.58 6.90e-01 2.10e+00 2.69e+01 angle pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" O GLY E 113 " ideal model delta sigma weight residual 122.29 118.11 4.18 8.10e-01 1.52e+00 2.67e+01 angle pdb=" CA GLY C 113 " pdb=" C GLY C 113 " pdb=" O GLY C 113 " ideal model delta sigma weight residual 122.29 118.11 4.18 8.10e-01 1.52e+00 2.66e+01 angle pdb=" C PHE E 54 " pdb=" N TRP E 55 " pdb=" CA TRP E 55 " ideal model delta sigma weight residual 120.38 127.28 -6.90 1.37e+00 5.33e-01 2.54e+01 ... (remaining 9333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 3542 13.92 - 27.85: 371 27.85 - 41.77: 87 41.77 - 55.70: 20 55.70 - 69.62: 14 Dihedral angle restraints: 4034 sinusoidal: 1574 harmonic: 2460 Sorted by residual: dihedral pdb=" CB CYS B 50 " pdb=" SG CYS B 50 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 151.19 -58.19 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 59 " pdb=" CB CYS A 59 " ideal model delta sinusoidal sigma weight residual 93.00 151.16 -58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CA LEU B 58 " pdb=" C LEU B 58 " pdb=" N CYS B 59 " pdb=" CA CYS B 59 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 4031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 395 0.043 - 0.086: 310 0.086 - 0.129: 221 0.129 - 0.172: 90 0.172 - 0.215: 20 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CA ILE F 33 " pdb=" N ILE F 33 " pdb=" C ILE F 33 " pdb=" CB ILE F 33 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE D 33 " pdb=" N ILE D 33 " pdb=" C ILE D 33 " pdb=" CB ILE D 33 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE C 84 " pdb=" N ILE C 84 " pdb=" C ILE C 84 " pdb=" CB ILE C 84 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1033 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 86 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ALA A 86 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA A 86 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP A 87 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 86 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C ALA B 86 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA B 86 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP B 87 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 93 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ARG B 93 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG B 93 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 94 " 0.012 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1664 2.87 - 3.38: 6811 3.38 - 3.89: 11017 3.89 - 4.39: 13006 4.39 - 4.90: 22414 Nonbonded interactions: 54912 Sorted by model distance: nonbonded pdb=" O PRO B 91 " pdb=" OG1 THR B 95 " model vdw 2.368 3.040 nonbonded pdb=" NH2 ARG E 99 " pdb=" OD2 ASP E 108 " model vdw 2.394 3.120 nonbonded pdb=" NH2 ARG C 99 " pdb=" OD2 ASP C 108 " model vdw 2.395 3.120 nonbonded pdb=" O ILE B 104 " pdb=" OG1 THR B 108 " model vdw 2.486 3.040 nonbonded pdb=" O ILE A 104 " pdb=" OG1 THR A 108 " model vdw 2.487 3.040 ... (remaining 54907 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 2.100 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 : 0.014 0.175 6898 Z= 1.050 Angle : 1.712 7.637 9346 Z= 1.277 Chirality : 0.080 0.215 1036 Planarity : 0.004 0.039 1148 Dihedral : 12.725 69.621 2450 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.27 % Allowed : 5.74 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.27), residues: 840 helix: -1.20 (0.24), residues: 302 sheet: -0.35 (0.34), residues: 182 loop : -0.63 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.024 0.003 TYR A 144 PHE 0.029 0.003 PHE B 46 TRP 0.019 0.003 TRP E 110 HIS 0.007 0.002 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.01364 ( 6888) covalent geometry : angle 1.70998 ( 9338) SS BOND : bond 0.00548 ( 4) SS BOND : angle 3.10718 ( 8) hydrogen bonds : bond 0.20411 ( 368) hydrogen bonds : angle 8.90982 ( 1014) metal coordination : bond 0.14203 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7361 (mmm160) cc_final: 0.7048 (mtm-85) REVERT: A 138 LYS cc_start: 0.7683 (mptt) cc_final: 0.7028 (mtpp) REVERT: B 29 ARG cc_start: 0.7380 (mmm160) cc_final: 0.7130 (mtm-85) REVERT: B 138 LYS cc_start: 0.7669 (mptt) cc_final: 0.7017 (mtpp) REVERT: C 48 GLU cc_start: 0.7563 (tt0) cc_final: 0.7358 (tt0) REVERT: C 94 THR cc_start: 0.7716 (p) cc_final: 0.7253 (p) REVERT: D 14 SER cc_start: 0.7686 (p) cc_final: 0.7309 (m) REVERT: E 94 THR cc_start: 0.7710 (p) cc_final: 0.7262 (p) REVERT: F 45 ARG cc_start: 0.7436 (mtp85) cc_final: 0.7225 (mtp85) outliers start: 2 outliers final: 2 residues processed: 151 average time/residue: 0.0766 time to fit residues: 15.1846 Evaluate side-chains 118 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain F residue 61 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 92 GLN D 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.186298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154704 restraints weight = 7504.656| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.64 r_work: 0.3681 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6898 Z= 0.156 Angle : 0.613 6.573 9346 Z= 0.323 Chirality : 0.043 0.156 1036 Planarity : 0.004 0.033 1148 Dihedral : 5.733 59.367 932 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.64 % Allowed : 10.93 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.29), residues: 840 helix: 1.19 (0.29), residues: 302 sheet: -0.59 (0.33), residues: 226 loop : 0.02 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 68 TYR 0.014 0.002 TYR A 72 PHE 0.014 0.002 PHE A 69 TRP 0.008 0.001 TRP C 55 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6888) covalent geometry : angle 0.61085 ( 9338) SS BOND : bond 0.00114 ( 4) SS BOND : angle 1.84074 ( 8) hydrogen bonds : bond 0.04523 ( 368) hydrogen bonds : angle 5.21805 ( 1014) metal coordination : bond 0.00623 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8161 (mptt) cc_final: 0.7806 (mtpp) REVERT: B 138 LYS cc_start: 0.8161 (mptt) cc_final: 0.7722 (mtpp) REVERT: C 107 MET cc_start: 0.8526 (ptp) cc_final: 0.8172 (ptp) outliers start: 12 outliers final: 10 residues processed: 119 average time/residue: 0.0766 time to fit residues: 11.9612 Evaluate side-chains 121 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.184584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145300 restraints weight = 7395.599| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.99 r_work: 0.3622 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6898 Z= 0.144 Angle : 0.557 5.937 9346 Z= 0.293 Chirality : 0.043 0.207 1036 Planarity : 0.004 0.032 1148 Dihedral : 5.172 53.265 932 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.91 % Allowed : 11.61 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.29), residues: 840 helix: 1.67 (0.29), residues: 302 sheet: -0.16 (0.35), residues: 216 loop : 0.03 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 68 TYR 0.013 0.001 TYR B 72 PHE 0.014 0.001 PHE A 39 TRP 0.008 0.001 TRP C 110 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6888) covalent geometry : angle 0.55487 ( 9338) SS BOND : bond 0.00069 ( 4) SS BOND : angle 1.60874 ( 8) hydrogen bonds : bond 0.04201 ( 368) hydrogen bonds : angle 4.72825 ( 1014) metal coordination : bond 0.00112 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8122 (mptt) cc_final: 0.7662 (mtpp) REVERT: B 138 LYS cc_start: 0.8103 (mptt) cc_final: 0.7638 (mtpp) outliers start: 14 outliers final: 9 residues processed: 114 average time/residue: 0.0732 time to fit residues: 11.1789 Evaluate side-chains 113 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 42 optimal weight: 0.0470 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN D 90 GLN F 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.192985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158155 restraints weight = 7357.203| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.78 r_work: 0.3680 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6898 Z= 0.117 Angle : 0.523 7.576 9346 Z= 0.271 Chirality : 0.041 0.169 1036 Planarity : 0.004 0.030 1148 Dihedral : 4.811 47.796 932 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.91 % Allowed : 11.89 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.30), residues: 840 helix: 1.96 (0.29), residues: 302 sheet: 0.25 (0.36), residues: 216 loop : 0.05 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 68 TYR 0.010 0.001 TYR B 72 PHE 0.013 0.001 PHE B 39 TRP 0.007 0.001 TRP A 113 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6888) covalent geometry : angle 0.52163 ( 9338) SS BOND : bond 0.00014 ( 4) SS BOND : angle 1.37786 ( 8) hydrogen bonds : bond 0.03886 ( 368) hydrogen bonds : angle 4.45599 ( 1014) metal coordination : bond 0.00101 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8148 (mptt) cc_final: 0.7752 (mtpp) REVERT: B 138 LYS cc_start: 0.8113 (mptt) cc_final: 0.7726 (mtpp) REVERT: C 107 MET cc_start: 0.8438 (ptp) cc_final: 0.7954 (ptp) outliers start: 14 outliers final: 4 residues processed: 123 average time/residue: 0.0733 time to fit residues: 12.1411 Evaluate side-chains 115 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 54 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.0010 chunk 6 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.194294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.162100 restraints weight = 7332.648| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.63 r_work: 0.3713 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6898 Z= 0.120 Angle : 0.522 7.064 9346 Z= 0.270 Chirality : 0.041 0.142 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.101 22.698 924 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.78 % Allowed : 13.80 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.30), residues: 840 helix: 2.00 (0.29), residues: 304 sheet: 0.53 (0.36), residues: 220 loop : -0.05 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 68 TYR 0.011 0.001 TYR B 72 PHE 0.013 0.001 PHE A 39 TRP 0.008 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6888) covalent geometry : angle 0.52038 ( 9338) SS BOND : bond 0.00044 ( 4) SS BOND : angle 1.28855 ( 8) hydrogen bonds : bond 0.03891 ( 368) hydrogen bonds : angle 4.32032 ( 1014) metal coordination : bond 0.00121 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8103 (mptt) cc_final: 0.7768 (mtpp) REVERT: B 138 LYS cc_start: 0.8075 (mptt) cc_final: 0.7740 (mtpp) REVERT: C 107 MET cc_start: 0.8372 (ptp) cc_final: 0.7819 (ptp) REVERT: E 72 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7927 (p) REVERT: E 107 MET cc_start: 0.8429 (ptp) cc_final: 0.7893 (ptp) outliers start: 13 outliers final: 5 residues processed: 120 average time/residue: 0.0943 time to fit residues: 15.1253 Evaluate side-chains 116 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.181541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.149736 restraints weight = 7589.124| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.64 r_work: 0.3660 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6898 Z= 0.164 Angle : 0.565 6.641 9346 Z= 0.289 Chirality : 0.042 0.130 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.211 25.312 924 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.19 % Allowed : 14.34 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.29), residues: 840 helix: 1.91 (0.29), residues: 300 sheet: 0.40 (0.36), residues: 216 loop : -0.26 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.015 0.002 TYR F 91 PHE 0.014 0.002 PHE B 39 TRP 0.012 0.001 TRP C 110 HIS 0.002 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 6888) covalent geometry : angle 0.56351 ( 9338) SS BOND : bond 0.00132 ( 4) SS BOND : angle 1.34553 ( 8) hydrogen bonds : bond 0.04206 ( 368) hydrogen bonds : angle 4.46655 ( 1014) metal coordination : bond 0.00202 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8163 (mptt) cc_final: 0.7775 (mtpp) REVERT: B 138 LYS cc_start: 0.8139 (mptt) cc_final: 0.7757 (mtpp) outliers start: 16 outliers final: 8 residues processed: 117 average time/residue: 0.1013 time to fit residues: 15.4657 Evaluate side-chains 117 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.184428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.153099 restraints weight = 7510.980| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.64 r_work: 0.3691 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6898 Z= 0.119 Angle : 0.523 6.170 9346 Z= 0.266 Chirality : 0.040 0.134 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.054 24.628 924 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 13.93 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.30), residues: 840 helix: 2.08 (0.29), residues: 300 sheet: 0.64 (0.37), residues: 220 loop : -0.30 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 68 TYR 0.010 0.001 TYR B 72 PHE 0.012 0.001 PHE B 39 TRP 0.009 0.001 TRP A 113 HIS 0.002 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6888) covalent geometry : angle 0.52198 ( 9338) SS BOND : bond 0.00047 ( 4) SS BOND : angle 1.27162 ( 8) hydrogen bonds : bond 0.03819 ( 368) hydrogen bonds : angle 4.28637 ( 1014) metal coordination : bond 0.00094 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8085 (mptt) cc_final: 0.7704 (mtpp) REVERT: B 138 LYS cc_start: 0.8097 (mptt) cc_final: 0.7716 (mtpp) REVERT: E 83 MET cc_start: 0.7050 (mpp) cc_final: 0.6822 (mmt) outliers start: 13 outliers final: 4 residues processed: 126 average time/residue: 0.0788 time to fit residues: 13.4036 Evaluate side-chains 115 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 33 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.185320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157564 restraints weight = 7545.958| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.56 r_work: 0.3717 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6898 Z= 0.115 Angle : 0.530 8.839 9346 Z= 0.267 Chirality : 0.040 0.135 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.009 24.810 924 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.64 % Allowed : 14.89 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.30), residues: 840 helix: 2.17 (0.29), residues: 300 sheet: 0.68 (0.37), residues: 220 loop : -0.29 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 68 TYR 0.010 0.001 TYR B 72 PHE 0.012 0.001 PHE B 39 TRP 0.012 0.001 TRP A 113 HIS 0.002 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6888) covalent geometry : angle 0.52927 ( 9338) SS BOND : bond 0.00041 ( 4) SS BOND : angle 1.24735 ( 8) hydrogen bonds : bond 0.03784 ( 368) hydrogen bonds : angle 4.21350 ( 1014) metal coordination : bond 0.00112 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8008 (mptt) cc_final: 0.7691 (mtpp) REVERT: B 138 LYS cc_start: 0.8045 (mptt) cc_final: 0.7719 (mtpp) REVERT: D 11 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7348 (tt) outliers start: 12 outliers final: 3 residues processed: 121 average time/residue: 0.0845 time to fit residues: 13.9132 Evaluate side-chains 115 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.193189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156715 restraints weight = 7425.130| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.87 r_work: 0.3698 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6898 Z= 0.126 Angle : 0.562 11.944 9346 Z= 0.277 Chirality : 0.041 0.137 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.051 25.528 924 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 14.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.30), residues: 840 helix: 2.15 (0.29), residues: 300 sheet: 0.64 (0.37), residues: 220 loop : -0.32 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 68 TYR 0.010 0.001 TYR B 72 PHE 0.013 0.001 PHE A 39 TRP 0.012 0.001 TRP B 113 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6888) covalent geometry : angle 0.56155 ( 9338) SS BOND : bond 0.00050 ( 4) SS BOND : angle 1.19917 ( 8) hydrogen bonds : bond 0.03842 ( 368) hydrogen bonds : angle 4.24144 ( 1014) metal coordination : bond 0.00130 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8114 (mptt) cc_final: 0.7727 (mtpp) REVERT: B 138 LYS cc_start: 0.8105 (mptt) cc_final: 0.7721 (mtpp) REVERT: D 11 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7381 (tt) REVERT: F 11 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7468 (tt) outliers start: 13 outliers final: 7 residues processed: 115 average time/residue: 0.0881 time to fit residues: 13.6756 Evaluate side-chains 116 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 13 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.192079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160357 restraints weight = 7421.020| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.61 r_work: 0.3317 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6898 Z= 0.127 Angle : 0.552 10.042 9346 Z= 0.275 Chirality : 0.041 0.136 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.073 26.365 924 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.50 % Allowed : 15.16 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.29), residues: 840 helix: 2.10 (0.29), residues: 302 sheet: 0.61 (0.37), residues: 220 loop : -0.47 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 68 TYR 0.012 0.001 TYR A 150 PHE 0.013 0.001 PHE B 39 TRP 0.013 0.001 TRP B 113 HIS 0.002 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6888) covalent geometry : angle 0.55141 ( 9338) SS BOND : bond 0.00050 ( 4) SS BOND : angle 1.17492 ( 8) hydrogen bonds : bond 0.03857 ( 368) hydrogen bonds : angle 4.27012 ( 1014) metal coordination : bond 0.00133 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8021 (mptt) cc_final: 0.7613 (mtpp) REVERT: B 138 LYS cc_start: 0.8025 (mptt) cc_final: 0.7622 (mtpp) REVERT: D 11 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7246 (tt) REVERT: E 83 MET cc_start: 0.7006 (mpp) cc_final: 0.6668 (mmt) REVERT: F 11 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7205 (tt) outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 0.0882 time to fit residues: 13.2293 Evaluate side-chains 110 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN D 6 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.180535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143665 restraints weight = 7592.464| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.84 r_work: 0.3660 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6898 Z= 0.125 Angle : 0.547 9.679 9346 Z= 0.273 Chirality : 0.041 0.137 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.038 26.476 924 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 14.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.29), residues: 840 helix: 2.16 (0.29), residues: 300 sheet: 0.65 (0.37), residues: 220 loop : -0.47 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 68 TYR 0.010 0.001 TYR B 72 PHE 0.013 0.001 PHE B 39 TRP 0.013 0.001 TRP B 113 HIS 0.002 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6888) covalent geometry : angle 0.54652 ( 9338) SS BOND : bond 0.00055 ( 4) SS BOND : angle 1.16714 ( 8) hydrogen bonds : bond 0.03816 ( 368) hydrogen bonds : angle 4.26219 ( 1014) metal coordination : bond 0.00132 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1795.22 seconds wall clock time: 31 minutes 37.01 seconds (1897.01 seconds total)