Starting phenix.real_space_refine on Fri Aug 22 18:15:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t06_40936/08_2025/8t06_40936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t06_40936/08_2025/8t06_40936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t06_40936/08_2025/8t06_40936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t06_40936/08_2025/8t06_40936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t06_40936/08_2025/8t06_40936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t06_40936/08_2025/8t06_40936.map" } resolution = 3.32 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= 0.054 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 4358 2.51 5 N 1084 2.21 5 O 1224 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: 6712 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1587 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "B" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1587 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, '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: 1.74, per 1000 atoms: 0.26 Number of scatterers: 6712 At special positions: 0 Unit cell: (87.15, 108.73, 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 1224 8.00 N 1084 7.00 C 4358 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: 0.56 Conformation dependent library (CDL) restraints added in 344.1 milliseconds Enol-peptide restraints added in 953.7 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 180 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " 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: 30 helices and 12 sheets defined 43.5% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 4.285A 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 52 removed outlier: 3.970A pdb=" N ASP A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 86 removed outlier: 3.519A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 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 178 through 194 Processing helix chain 'A' and resid 199 through 203 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 52 removed outlier: 3.969A pdb=" N ASP B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 86 removed outlier: 3.519A pdb=" N LEU B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 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 178 through 194 Processing helix chain 'B' and resid 199 through 203 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 88 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.566A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) 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 88 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.567A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) 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: 6.980A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.653A 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: 3.849A 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 14 removed outlier: 6.719A 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 14 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: 6.980A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.653A 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: 3.849A 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 14 removed outlier: 6.721A 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 14 398 hydrogen bonds defined for protein. 1074 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: 1.05 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1251 1.34 - 1.46: 1807 1.46 - 1.58: 3762 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 6892 Sorted by residual: bond pdb=" N ILE D 29 " pdb=" CA ILE D 29 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.09e-02 8.42e+03 1.39e+01 bond pdb=" N ILE F 29 " pdb=" CA ILE F 29 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.09e-02 8.42e+03 1.38e+01 bond pdb=" N ILE D 58 " pdb=" CA ILE D 58 " ideal model delta sigma weight residual 1.462 1.496 -0.035 1.01e-02 9.80e+03 1.18e+01 bond pdb=" N VAL A 198 " pdb=" CA VAL A 198 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.14e-02 7.69e+03 1.13e+01 bond pdb=" N SER D 7 " pdb=" CA SER D 7 " ideal model delta sigma weight residual 1.462 1.488 -0.026 7.70e-03 1.69e+04 1.12e+01 ... (remaining 6887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 5347 1.32 - 2.64: 2720 2.64 - 3.96: 1034 3.96 - 5.29: 225 5.29 - 6.61: 20 Bond angle restraints: 9346 Sorted by residual: angle pdb=" C PHE C 54 " pdb=" N TRP C 55 " pdb=" CA TRP C 55 " ideal model delta sigma weight residual 120.38 126.99 -6.61 1.37e+00 5.33e-01 2.33e+01 angle pdb=" C PHE E 54 " pdb=" N TRP E 55 " pdb=" CA TRP E 55 " ideal model delta sigma weight residual 120.38 126.96 -6.58 1.37e+00 5.33e-01 2.31e+01 angle pdb=" C PHE B 160 " pdb=" N GLY B 161 " pdb=" CA GLY B 161 " ideal model delta sigma weight residual 119.94 124.87 -4.93 1.11e+00 8.12e-01 1.97e+01 angle pdb=" C TYR A 115 " pdb=" N GLY A 116 " pdb=" CA GLY A 116 " ideal model delta sigma weight residual 120.13 125.70 -5.57 1.26e+00 6.30e-01 1.95e+01 angle pdb=" C TYR B 115 " pdb=" N GLY B 116 " pdb=" CA GLY B 116 " ideal model delta sigma weight residual 120.13 125.67 -5.54 1.26e+00 6.30e-01 1.93e+01 ... (remaining 9341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 3624 16.05 - 32.10: 326 32.10 - 48.15: 52 48.15 - 64.20: 26 64.20 - 80.25: 2 Dihedral angle restraints: 4030 sinusoidal: 1568 harmonic: 2462 Sorted by residual: dihedral pdb=" CA PHE B 170 " pdb=" C PHE B 170 " pdb=" N PHE B 171 " pdb=" CA PHE B 171 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE A 170 " pdb=" C PHE A 170 " pdb=" N PHE A 171 " pdb=" CA PHE A 171 " ideal model delta harmonic sigma weight residual 180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA CYS B 59 " pdb=" C CYS B 59 " pdb=" N PHE B 60 " pdb=" CA PHE B 60 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 4027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 430 0.046 - 0.092: 319 0.092 - 0.138: 207 0.138 - 0.184: 68 0.184 - 0.230: 12 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CA ILE E 39 " pdb=" N ILE E 39 " pdb=" C ILE E 39 " pdb=" CB ILE E 39 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE C 39 " pdb=" N ILE C 39 " pdb=" C ILE C 39 " pdb=" CB ILE C 39 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE F 21 " pdb=" N ILE F 21 " pdb=" C ILE F 21 " pdb=" CB ILE F 21 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1033 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 144 " -0.021 2.00e-02 2.50e+03 1.21e-02 2.92e+00 pdb=" CG TYR A 144 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 144 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 144 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 144 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 144 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 144 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 144 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 144 " 0.021 2.00e-02 2.50e+03 1.20e-02 2.90e+00 pdb=" CG TYR B 144 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 144 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 144 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 144 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 144 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 144 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 144 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 50 " 0.013 2.00e-02 2.50e+03 1.08e-02 2.35e+00 pdb=" CG TYR F 50 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR F 50 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR F 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR F 50 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 50 " 0.001 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2961 2.99 - 3.47: 6785 3.47 - 3.94: 11304 3.94 - 4.42: 12527 4.42 - 4.90: 21451 Nonbonded interactions: 55028 Sorted by model distance: nonbonded pdb=" O ASP F 82 " pdb=" OH TYR F 86 " model vdw 2.510 3.040 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.511 3.040 nonbonded pdb=" NH2 ARG C 99 " pdb=" OD2 ASP C 108 " model vdw 2.528 3.120 nonbonded pdb=" N TYR D 50 " pdb=" O TYR D 50 " model vdw 2.528 2.496 nonbonded pdb=" O MET E 107 " pdb=" OH TYR F 36 " model vdw 2.528 3.040 ... (remaining 55023 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: 2.020 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: 0.020 Set scattering table: 0.020 Process input model: 8.990 Find NCS groups from input model: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 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 0.165 6902 Z= 1.049 Angle : 1.727 6.607 9354 Z= 1.286 Chirality : 0.081 0.230 1036 Planarity : 0.003 0.023 1148 Dihedral : 13.195 80.246 2446 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.96 % Allowed : 5.60 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.29), residues: 840 helix: -1.58 (0.25), residues: 284 sheet: 0.56 (0.36), residues: 184 loop : -0.01 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 68 TYR 0.027 0.003 TYR F 50 PHE 0.023 0.003 PHE B 43 TRP 0.024 0.003 TRP E 110 HIS 0.008 0.002 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.01364 ( 6892) covalent geometry : angle 1.72662 ( 9346) SS BOND : bond 0.00444 ( 4) SS BOND : angle 2.44237 ( 8) hydrogen bonds : bond 0.18962 ( 376) hydrogen bonds : angle 8.83674 ( 1074) metal coordination : bond 0.13243 ( 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 232 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6557 (t80) cc_final: 0.6314 (m-10) REVERT: A 63 ARG cc_start: 0.7542 (mtp85) cc_final: 0.7125 (mmm-85) REVERT: A 67 GLU cc_start: 0.7829 (tt0) cc_final: 0.7592 (tt0) REVERT: A 109 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.6898 (m-80) REVERT: B 42 PHE cc_start: 0.6594 (t80) cc_final: 0.6310 (m-10) REVERT: B 63 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7163 (mmm-85) REVERT: B 67 GLU cc_start: 0.7849 (tt0) cc_final: 0.7605 (tt0) REVERT: B 109 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: B 168 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6640 (tpt-90) REVERT: C 65 LEU cc_start: 0.8359 (mt) cc_final: 0.8066 (mt) REVERT: C 69 LEU cc_start: 0.7860 (mp) cc_final: 0.7640 (mt) REVERT: C 73 LYS cc_start: 0.8458 (ptmm) cc_final: 0.8212 (ptmm) REVERT: C 99 ARG cc_start: 0.7521 (ttp-170) cc_final: 0.6798 (tmm-80) REVERT: C 102 TRP cc_start: 0.7553 (t60) cc_final: 0.7352 (t-100) REVERT: C 108 ASP cc_start: 0.7791 (p0) cc_final: 0.7009 (p0) REVERT: D 22 THR cc_start: 0.7914 (m) cc_final: 0.7640 (p) REVERT: D 42 LYS cc_start: 0.8030 (mttp) cc_final: 0.7577 (mmtp) REVERT: D 82 ASP cc_start: 0.7584 (m-30) cc_final: 0.7270 (m-30) REVERT: D 105 GLU cc_start: 0.6745 (tt0) cc_final: 0.6531 (tm-30) REVERT: E 52 HIS cc_start: 0.8054 (m170) cc_final: 0.7649 (m90) REVERT: E 69 LEU cc_start: 0.7882 (mp) cc_final: 0.7653 (mt) REVERT: E 73 LYS cc_start: 0.8528 (ptmm) cc_final: 0.8236 (ptmm) REVERT: E 99 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.6805 (tmm-80) REVERT: E 108 ASP cc_start: 0.7809 (p0) cc_final: 0.7050 (p0) REVERT: F 22 THR cc_start: 0.7905 (m) cc_final: 0.7656 (p) REVERT: F 42 LYS cc_start: 0.8060 (mttp) cc_final: 0.7605 (mmtp) REVERT: F 82 ASP cc_start: 0.7574 (m-30) cc_final: 0.7270 (m-30) outliers start: 7 outliers final: 4 residues processed: 232 average time/residue: 0.0989 time to fit residues: 29.4353 Evaluate side-chains 201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 194 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.0042 ------------------------------------------------------------------------------- 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 27 GLN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.161268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118718 restraints weight = 9109.253| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.71 r_work: 0.3163 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6902 Z= 0.157 Angle : 0.639 5.886 9354 Z= 0.332 Chirality : 0.044 0.154 1036 Planarity : 0.004 0.031 1148 Dihedral : 6.848 54.023 940 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.87 % Allowed : 11.75 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.30), residues: 840 helix: 0.99 (0.29), residues: 290 sheet: 0.83 (0.35), residues: 224 loop : 0.62 (0.40), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.015 0.001 TYR D 91 PHE 0.019 0.002 PHE A 43 TRP 0.009 0.001 TRP F 35 HIS 0.003 0.001 HIS B 48 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6892) covalent geometry : angle 0.63799 ( 9346) SS BOND : bond 0.00110 ( 4) SS BOND : angle 1.42058 ( 8) hydrogen bonds : bond 0.04636 ( 376) hydrogen bonds : angle 5.06602 ( 1074) metal coordination : bond 0.00311 ( 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 228 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8319 (tt0) cc_final: 0.8111 (tt0) REVERT: A 109 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: A 178 TYR cc_start: 0.7839 (m-80) cc_final: 0.7549 (m-80) REVERT: B 67 GLU cc_start: 0.8318 (tt0) cc_final: 0.8110 (tt0) REVERT: B 109 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: B 178 TYR cc_start: 0.7849 (m-80) cc_final: 0.7354 (m-80) REVERT: C 58 ASP cc_start: 0.8483 (t70) cc_final: 0.8136 (t0) REVERT: C 88 ASP cc_start: 0.7563 (t0) cc_final: 0.7271 (t70) REVERT: C 102 TRP cc_start: 0.8407 (t60) cc_final: 0.7772 (t-100) REVERT: C 108 ASP cc_start: 0.8877 (p0) cc_final: 0.8291 (p0) REVERT: C 109 TYR cc_start: 0.8626 (m-80) cc_final: 0.8362 (m-80) REVERT: E 58 ASP cc_start: 0.8493 (t70) cc_final: 0.8118 (t0) REVERT: E 108 ASP cc_start: 0.8871 (p0) cc_final: 0.8291 (p0) REVERT: E 109 TYR cc_start: 0.8614 (m-80) cc_final: 0.8357 (m-80) outliers start: 21 outliers final: 10 residues processed: 214 average time/residue: 0.1016 time to fit residues: 27.8833 Evaluate side-chains 198 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN D 77 ASN E 16 GLN F 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112534 restraints weight = 9070.721| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.63 r_work: 0.3084 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6902 Z= 0.226 Angle : 0.653 8.420 9354 Z= 0.337 Chirality : 0.046 0.148 1036 Planarity : 0.005 0.035 1148 Dihedral : 6.738 55.551 936 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.55 % Allowed : 13.11 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.30), residues: 840 helix: 1.41 (0.29), residues: 288 sheet: 1.00 (0.36), residues: 224 loop : 0.65 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.016 0.002 TYR B 72 PHE 0.024 0.002 PHE B 39 TRP 0.012 0.002 TRP C 110 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 6892) covalent geometry : angle 0.65201 ( 9346) SS BOND : bond 0.00379 ( 4) SS BOND : angle 1.51120 ( 8) hydrogen bonds : bond 0.04938 ( 376) hydrogen bonds : angle 4.85908 ( 1074) metal coordination : bond 0.00317 ( 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 224 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8192 (mmm-85) REVERT: A 109 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: A 178 TYR cc_start: 0.7920 (m-80) cc_final: 0.7613 (m-80) REVERT: B 63 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.8191 (mmm-85) REVERT: B 109 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: B 178 TYR cc_start: 0.7890 (m-80) cc_final: 0.7599 (m-80) REVERT: C 88 ASP cc_start: 0.7621 (t0) cc_final: 0.7352 (t70) REVERT: E 83 MET cc_start: 0.7524 (mpp) cc_final: 0.7286 (mpp) REVERT: F 105 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6601 (tm-30) outliers start: 26 outliers final: 16 residues processed: 212 average time/residue: 0.1003 time to fit residues: 27.3487 Evaluate side-chains 208 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS B 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108928 restraints weight = 9158.401| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.70 r_work: 0.3156 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6902 Z= 0.166 Angle : 0.612 9.693 9354 Z= 0.310 Chirality : 0.045 0.146 1036 Planarity : 0.004 0.034 1148 Dihedral : 6.537 56.717 936 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.42 % Allowed : 14.34 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.31), residues: 840 helix: 1.90 (0.29), residues: 284 sheet: 1.15 (0.36), residues: 224 loop : 0.58 (0.40), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.013 0.001 TYR D 91 PHE 0.018 0.001 PHE A 39 TRP 0.011 0.001 TRP E 110 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6892) covalent geometry : angle 0.61133 ( 9346) SS BOND : bond 0.00184 ( 4) SS BOND : angle 1.35550 ( 8) hydrogen bonds : bond 0.04280 ( 376) hydrogen bonds : angle 4.65947 ( 1074) metal coordination : bond 0.00205 ( 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 216 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: A 178 TYR cc_start: 0.7898 (m-80) cc_final: 0.7585 (m-80) REVERT: B 109 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: B 178 TYR cc_start: 0.7865 (m-80) cc_final: 0.7555 (m-80) REVERT: C 88 ASP cc_start: 0.7626 (t0) cc_final: 0.7284 (t70) REVERT: D 107 LYS cc_start: 0.5039 (tptt) cc_final: 0.4781 (tptt) REVERT: E 41 LYS cc_start: 0.9175 (tttm) cc_final: 0.8963 (tptp) REVERT: E 83 MET cc_start: 0.7488 (mpp) cc_final: 0.7264 (mpp) REVERT: E 88 ASP cc_start: 0.7621 (t0) cc_final: 0.7299 (t70) REVERT: F 105 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6738 (tm-30) outliers start: 25 outliers final: 7 residues processed: 200 average time/residue: 0.1008 time to fit residues: 25.8387 Evaluate side-chains 190 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.158969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110701 restraints weight = 9143.665| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.68 r_work: 0.3173 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6902 Z= 0.137 Angle : 0.596 9.737 9354 Z= 0.297 Chirality : 0.044 0.154 1036 Planarity : 0.004 0.035 1148 Dihedral : 5.928 54.120 932 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.78 % Allowed : 16.53 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.31), residues: 840 helix: 2.06 (0.29), residues: 296 sheet: 1.40 (0.36), residues: 216 loop : 0.60 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 63 TYR 0.010 0.001 TYR D 91 PHE 0.016 0.001 PHE B 39 TRP 0.011 0.001 TRP E 110 HIS 0.007 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6892) covalent geometry : angle 0.59456 ( 9346) SS BOND : bond 0.00863 ( 4) SS BOND : angle 1.41265 ( 8) hydrogen bonds : bond 0.03975 ( 376) hydrogen bonds : angle 4.47452 ( 1074) metal coordination : bond 0.00141 ( 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 209 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: A 170 PHE cc_start: 0.7590 (m-10) cc_final: 0.7317 (m-10) REVERT: A 178 TYR cc_start: 0.7894 (m-80) cc_final: 0.7547 (m-80) REVERT: B 109 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: B 170 PHE cc_start: 0.7569 (m-10) cc_final: 0.7264 (m-10) REVERT: B 178 TYR cc_start: 0.7844 (m-80) cc_final: 0.7352 (m-80) REVERT: C 16 GLN cc_start: 0.7626 (tt0) cc_final: 0.7014 (mt0) REVERT: C 41 LYS cc_start: 0.9139 (tptm) cc_final: 0.8923 (tptp) REVERT: C 88 ASP cc_start: 0.7583 (t0) cc_final: 0.7285 (t70) REVERT: C 102 TRP cc_start: 0.8506 (t60) cc_final: 0.7751 (t-100) REVERT: D 105 GLU cc_start: 0.6515 (tm-30) cc_final: 0.6144 (tm-30) REVERT: D 107 LYS cc_start: 0.4906 (tptt) cc_final: 0.4671 (tptt) REVERT: E 16 GLN cc_start: 0.7627 (tt0) cc_final: 0.7019 (mt0) REVERT: E 41 LYS cc_start: 0.9156 (tttm) cc_final: 0.8952 (tptp) REVERT: E 83 MET cc_start: 0.7374 (mpp) cc_final: 0.7146 (mpp) REVERT: E 88 ASP cc_start: 0.7543 (t0) cc_final: 0.7240 (t70) outliers start: 13 outliers final: 7 residues processed: 200 average time/residue: 0.1037 time to fit residues: 26.5430 Evaluate side-chains 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3894 r_free = 0.3894 target = 0.158989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117104 restraints weight = 9122.521| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.55 r_work: 0.3173 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6902 Z= 0.140 Angle : 0.604 9.754 9354 Z= 0.302 Chirality : 0.044 0.157 1036 Planarity : 0.004 0.037 1148 Dihedral : 5.843 53.765 932 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.32 % Allowed : 16.94 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.31), residues: 840 helix: 2.34 (0.29), residues: 288 sheet: 1.20 (0.36), residues: 222 loop : 0.38 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 63 TYR 0.009 0.001 TYR A 72 PHE 0.016 0.001 PHE B 39 TRP 0.013 0.001 TRP E 102 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6892) covalent geometry : angle 0.60295 ( 9346) SS BOND : bond 0.00218 ( 4) SS BOND : angle 1.25766 ( 8) hydrogen bonds : bond 0.03947 ( 376) hydrogen bonds : angle 4.36010 ( 1074) metal coordination : bond 0.00149 ( 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 215 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 PHE cc_start: 0.7535 (m-10) cc_final: 0.7309 (m-10) REVERT: A 178 TYR cc_start: 0.7925 (m-80) cc_final: 0.7575 (m-80) REVERT: B 170 PHE cc_start: 0.7536 (m-10) cc_final: 0.7285 (m-10) REVERT: B 178 TYR cc_start: 0.7891 (m-80) cc_final: 0.7406 (m-80) REVERT: C 16 GLN cc_start: 0.7671 (tt0) cc_final: 0.7085 (mt0) REVERT: C 41 LYS cc_start: 0.9117 (tptm) cc_final: 0.8892 (tptp) REVERT: C 88 ASP cc_start: 0.7588 (t0) cc_final: 0.7330 (t70) REVERT: C 102 TRP cc_start: 0.8491 (t60) cc_final: 0.7798 (t-100) REVERT: D 105 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6456 (tm-30) REVERT: D 107 LYS cc_start: 0.4780 (tptt) cc_final: 0.4519 (tptt) REVERT: E 16 GLN cc_start: 0.7678 (tt0) cc_final: 0.7084 (mt0) REVERT: E 60 ARG cc_start: 0.8113 (tpp-160) cc_final: 0.7603 (ttm110) REVERT: E 83 MET cc_start: 0.7368 (mpp) cc_final: 0.7142 (mpp) REVERT: E 88 ASP cc_start: 0.7571 (t0) cc_final: 0.7324 (t70) outliers start: 17 outliers final: 12 residues processed: 206 average time/residue: 0.0942 time to fit residues: 24.4637 Evaluate side-chains 203 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.160829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119348 restraints weight = 9004.768| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.69 r_work: 0.3195 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6902 Z= 0.121 Angle : 0.594 9.654 9354 Z= 0.295 Chirality : 0.043 0.160 1036 Planarity : 0.004 0.038 1148 Dihedral : 5.737 52.004 932 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 18.44 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.31), residues: 840 helix: 2.49 (0.29), residues: 288 sheet: 1.22 (0.36), residues: 222 loop : 0.27 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.007 0.001 TYR C 96 PHE 0.014 0.001 PHE A 39 TRP 0.009 0.001 TRP C 110 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6892) covalent geometry : angle 0.59335 ( 9346) SS BOND : bond 0.00119 ( 4) SS BOND : angle 1.15718 ( 8) hydrogen bonds : bond 0.03752 ( 376) hydrogen bonds : angle 4.26801 ( 1074) metal coordination : bond 0.00109 ( 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 207 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 PHE cc_start: 0.7564 (m-10) cc_final: 0.7343 (m-10) REVERT: A 178 TYR cc_start: 0.7910 (m-80) cc_final: 0.7423 (m-80) REVERT: B 170 PHE cc_start: 0.7583 (m-10) cc_final: 0.7339 (m-10) REVERT: C 16 GLN cc_start: 0.7696 (tt0) cc_final: 0.7149 (mt0) REVERT: C 41 LYS cc_start: 0.9104 (tptm) cc_final: 0.8867 (tptp) REVERT: C 73 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8406 (ttmm) REVERT: C 88 ASP cc_start: 0.7550 (t0) cc_final: 0.7291 (t70) REVERT: D 105 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6450 (tm-30) REVERT: D 107 LYS cc_start: 0.4710 (tptt) cc_final: 0.4462 (tptt) REVERT: E 16 GLN cc_start: 0.7718 (tt0) cc_final: 0.7169 (mt0) REVERT: E 60 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7693 (ttm110) REVERT: E 88 ASP cc_start: 0.7566 (t0) cc_final: 0.7315 (t70) REVERT: F 105 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6437 (tm-30) REVERT: F 107 LYS cc_start: 0.4605 (tptt) cc_final: 0.4366 (tptt) outliers start: 13 outliers final: 9 residues processed: 199 average time/residue: 0.0819 time to fit residues: 21.0137 Evaluate side-chains 194 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 82 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.160723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119149 restraints weight = 9138.557| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.54 r_work: 0.3201 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6902 Z= 0.134 Angle : 0.606 9.719 9354 Z= 0.302 Chirality : 0.044 0.167 1036 Planarity : 0.004 0.039 1148 Dihedral : 5.179 52.163 928 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.64 % Allowed : 18.31 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.31), residues: 840 helix: 2.53 (0.29), residues: 288 sheet: 1.19 (0.36), residues: 224 loop : 0.26 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 63 TYR 0.009 0.001 TYR E 96 PHE 0.015 0.001 PHE B 39 TRP 0.011 0.001 TRP C 110 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6892) covalent geometry : angle 0.60454 ( 9346) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.42070 ( 8) hydrogen bonds : bond 0.03784 ( 376) hydrogen bonds : angle 4.28351 ( 1074) metal coordination : bond 0.00132 ( 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 203 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7926 (m-80) cc_final: 0.7577 (m-80) REVERT: B 170 PHE cc_start: 0.7559 (m-10) cc_final: 0.7332 (m-10) REVERT: B 178 TYR cc_start: 0.7890 (m-80) cc_final: 0.7433 (m-80) REVERT: C 16 GLN cc_start: 0.7681 (tt0) cc_final: 0.7157 (mt0) REVERT: C 88 ASP cc_start: 0.7548 (t0) cc_final: 0.7277 (t70) REVERT: D 105 GLU cc_start: 0.6840 (tm-30) cc_final: 0.6527 (tm-30) REVERT: D 107 LYS cc_start: 0.4767 (tptt) cc_final: 0.4383 (tptt) REVERT: E 60 ARG cc_start: 0.8214 (tpp-160) cc_final: 0.7739 (ttm110) REVERT: E 88 ASP cc_start: 0.7543 (t0) cc_final: 0.7306 (t70) REVERT: F 105 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6366 (tm-30) REVERT: F 107 LYS cc_start: 0.4629 (tptt) cc_final: 0.4423 (tptt) outliers start: 12 outliers final: 10 residues processed: 194 average time/residue: 0.0859 time to fit residues: 21.1018 Evaluate side-chains 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 68 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109979 restraints weight = 9051.415| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.66 r_work: 0.3164 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6902 Z= 0.178 Angle : 0.626 9.420 9354 Z= 0.317 Chirality : 0.045 0.196 1036 Planarity : 0.004 0.039 1148 Dihedral : 5.274 52.698 928 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.50 % Allowed : 18.72 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.31), residues: 840 helix: 2.37 (0.29), residues: 288 sheet: 1.17 (0.36), residues: 220 loop : 0.20 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 63 TYR 0.011 0.001 TYR D 91 PHE 0.019 0.001 PHE B 39 TRP 0.010 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6892) covalent geometry : angle 0.62533 ( 9346) SS BOND : bond 0.00177 ( 4) SS BOND : angle 1.23717 ( 8) hydrogen bonds : bond 0.04098 ( 376) hydrogen bonds : angle 4.42675 ( 1074) metal coordination : bond 0.00220 ( 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 202 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7943 (m-80) cc_final: 0.7570 (m-80) REVERT: B 170 PHE cc_start: 0.7619 (m-10) cc_final: 0.7385 (m-10) REVERT: B 178 TYR cc_start: 0.7895 (m-80) cc_final: 0.7557 (m-80) REVERT: C 16 GLN cc_start: 0.7794 (tt0) cc_final: 0.7242 (mt0) REVERT: C 88 ASP cc_start: 0.7593 (t0) cc_final: 0.7324 (t70) REVERT: D 105 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6630 (tm-30) REVERT: E 60 ARG cc_start: 0.8186 (tpp-160) cc_final: 0.7715 (ttm110) REVERT: E 88 ASP cc_start: 0.7595 (t0) cc_final: 0.7373 (t70) REVERT: F 79 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8610 (mm-30) REVERT: F 105 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6521 (tm-30) outliers start: 11 outliers final: 10 residues processed: 194 average time/residue: 0.0796 time to fit residues: 19.9529 Evaluate side-chains 202 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 68 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.159992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112189 restraints weight = 9008.754| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.62 r_work: 0.3196 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6902 Z= 0.149 Angle : 0.628 9.210 9354 Z= 0.315 Chirality : 0.044 0.196 1036 Planarity : 0.004 0.039 1148 Dihedral : 5.453 51.267 928 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.78 % Allowed : 18.99 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.31), residues: 840 helix: 2.42 (0.29), residues: 288 sheet: 1.36 (0.36), residues: 216 loop : 0.04 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 63 TYR 0.011 0.001 TYR F 91 PHE 0.016 0.001 PHE B 39 TRP 0.017 0.001 TRP B 113 HIS 0.002 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6892) covalent geometry : angle 0.62753 ( 9346) SS BOND : bond 0.00210 ( 4) SS BOND : angle 1.21127 ( 8) hydrogen bonds : bond 0.03874 ( 376) hydrogen bonds : angle 4.36178 ( 1074) metal coordination : bond 0.00165 ( 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 203 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7921 (m-80) cc_final: 0.7582 (m-80) REVERT: B 115 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6999 (p90) REVERT: B 170 PHE cc_start: 0.7611 (m-10) cc_final: 0.7396 (m-10) REVERT: B 178 TYR cc_start: 0.7888 (m-80) cc_final: 0.7572 (m-80) REVERT: C 16 GLN cc_start: 0.7809 (tt0) cc_final: 0.7284 (mt0) REVERT: C 66 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7481 (mttp) REVERT: C 88 ASP cc_start: 0.7561 (t0) cc_final: 0.7307 (t70) REVERT: D 105 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6590 (tm-30) REVERT: E 16 GLN cc_start: 0.7796 (tt0) cc_final: 0.7240 (mt0) REVERT: E 41 LYS cc_start: 0.9061 (tptm) cc_final: 0.8774 (tptt) REVERT: E 60 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7673 (ttm110) REVERT: E 88 ASP cc_start: 0.7580 (t0) cc_final: 0.7343 (t70) REVERT: F 105 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6525 (tm-30) outliers start: 13 outliers final: 11 residues processed: 193 average time/residue: 0.0809 time to fit residues: 20.2084 Evaluate side-chains 201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.161612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119597 restraints weight = 9004.065| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.59 r_work: 0.3212 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6902 Z= 0.128 Angle : 0.595 8.745 9354 Z= 0.301 Chirality : 0.044 0.202 1036 Planarity : 0.004 0.040 1148 Dihedral : 5.357 57.308 928 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.37 % Allowed : 18.99 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.31), residues: 840 helix: 2.51 (0.29), residues: 288 sheet: 1.33 (0.36), residues: 218 loop : 0.03 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 63 TYR 0.010 0.001 TYR C 96 PHE 0.014 0.001 PHE B 39 TRP 0.016 0.001 TRP B 113 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6892) covalent geometry : angle 0.59397 ( 9346) SS BOND : bond 0.00162 ( 4) SS BOND : angle 1.27268 ( 8) hydrogen bonds : bond 0.03689 ( 376) hydrogen bonds : angle 4.27246 ( 1074) metal coordination : bond 0.00108 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1700.18 seconds wall clock time: 29 minutes 56.22 seconds (1796.22 seconds total)