Starting phenix.real_space_refine on Sat May 10 19:12:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t06_40936/05_2025/8t06_40936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t06_40936/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t06_40936/05_2025/8t06_40936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t06_40936/05_2025/8t06_40936.map" model { file = "/net/cci-nas-00/data/ceres_data/8t06_40936/05_2025/8t06_40936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t06_40936/05_2025/8t06_40936.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.77, per 1000 atoms: 0.71 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: 1.50 Conformation dependent library (CDL) restraints added in 848.9 milliseconds 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: 0.79 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: 1.74 Time building geometry restraints manager: 1.77 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.470 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.003 TRP E 110 HIS 0.008 0.002 HIS D 49 PHE 0.023 0.003 PHE B 43 TYR 0.027 0.003 TYR F 50 ARG 0.002 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.18962 ( 376) hydrogen bonds : angle 8.83674 ( 1074) metal coordination : bond 0.13243 ( 6) SS BOND : bond 0.00444 ( 4) SS BOND : angle 2.44237 ( 8) covalent geometry : bond 0.01364 ( 6892) covalent geometry : angle 1.72662 ( 9346) *********************** 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 : 0.788 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: 0.2063 time to fit residues: 60.8880 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 : 0.671 ------------------------------------------------------------------------------- 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 69 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.161693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118502 restraints weight = 8936.767| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.54 r_work: 0.3182 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6902 Z= 0.149 Angle : 0.634 5.910 9354 Z= 0.330 Chirality : 0.044 0.154 1036 Planarity : 0.004 0.030 1148 Dihedral : 6.862 54.476 940 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.87 % Allowed : 11.61 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.30), residues: 840 helix: 1.05 (0.29), residues: 286 sheet: 0.80 (0.35), residues: 224 loop : 0.58 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 110 HIS 0.003 0.001 HIS C 52 PHE 0.018 0.002 PHE D 73 TYR 0.015 0.001 TYR D 91 ARG 0.002 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 376) hydrogen bonds : angle 5.10346 ( 1074) metal coordination : bond 0.00206 ( 6) SS BOND : bond 0.00059 ( 4) SS BOND : angle 1.38980 ( 8) covalent geometry : bond 0.00332 ( 6892) covalent geometry : angle 0.63341 ( 9346) *********************** 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 229 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7837 (m-80) cc_final: 0.7553 (m-80) REVERT: B 109 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: B 178 TYR cc_start: 0.7821 (m-80) cc_final: 0.7316 (m-80) REVERT: C 58 ASP cc_start: 0.8473 (t70) cc_final: 0.8112 (t0) REVERT: C 88 ASP cc_start: 0.7555 (t0) cc_final: 0.7332 (t70) REVERT: C 108 ASP cc_start: 0.8858 (p0) cc_final: 0.8264 (p0) REVERT: C 109 TYR cc_start: 0.8598 (m-80) cc_final: 0.8335 (m-80) REVERT: E 108 ASP cc_start: 0.8845 (p0) cc_final: 0.8247 (p0) REVERT: E 109 TYR cc_start: 0.8598 (m-80) cc_final: 0.8331 (m-80) outliers start: 21 outliers final: 11 residues processed: 215 average time/residue: 0.2032 time to fit residues: 55.9099 Evaluate side-chains 199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 27 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.0270 chunk 42 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 C 16 GLN D 77 ASN E 16 GLN F 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118520 restraints weight = 9067.958| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.53 r_work: 0.3200 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6902 Z= 0.121 Angle : 0.583 8.412 9354 Z= 0.295 Chirality : 0.043 0.148 1036 Planarity : 0.004 0.036 1148 Dihedral : 6.529 53.250 936 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.05 % Allowed : 13.66 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.31), residues: 840 helix: 1.82 (0.29), residues: 288 sheet: 1.19 (0.36), residues: 216 loop : 0.80 (0.40), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.003 0.001 HIS A 110 PHE 0.016 0.001 PHE A 43 TYR 0.011 0.001 TYR D 91 ARG 0.005 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 376) hydrogen bonds : angle 4.57289 ( 1074) metal coordination : bond 0.00111 ( 6) SS BOND : bond 0.00119 ( 4) SS BOND : angle 1.44424 ( 8) covalent geometry : bond 0.00269 ( 6892) covalent geometry : angle 0.58188 ( 9346) *********************** 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 207 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: A 178 TYR cc_start: 0.7800 (m-80) cc_final: 0.7318 (m-80) REVERT: B 109 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: B 178 TYR cc_start: 0.7798 (m-80) cc_final: 0.7305 (m-80) REVERT: C 58 ASP cc_start: 0.8312 (t70) cc_final: 0.8034 (t0) REVERT: C 88 ASP cc_start: 0.7574 (t0) cc_final: 0.7316 (t70) REVERT: D 77 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.6887 (m-40) REVERT: E 83 MET cc_start: 0.7618 (mpp) cc_final: 0.7241 (mpp) REVERT: F 77 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6906 (m-40) REVERT: F 105 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6525 (tm-30) outliers start: 15 outliers final: 8 residues processed: 199 average time/residue: 0.2187 time to fit residues: 55.5113 Evaluate side-chains 196 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 33 ILE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 77 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 D 77 ASN F 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.157377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109088 restraints weight = 9164.848| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.71 r_work: 0.3149 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3507 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= 0.182 Angle : 0.618 6.742 9354 Z= 0.316 Chirality : 0.045 0.154 1036 Planarity : 0.004 0.035 1148 Dihedral : 6.603 55.887 936 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.42 % Allowed : 13.93 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.30), residues: 840 helix: 1.92 (0.29), residues: 284 sheet: 1.11 (0.36), residues: 216 loop : 0.60 (0.39), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.003 0.001 HIS B 110 PHE 0.020 0.002 PHE A 39 TYR 0.013 0.001 TYR A 72 ARG 0.006 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 376) hydrogen bonds : angle 4.52892 ( 1074) metal coordination : bond 0.00231 ( 6) SS BOND : bond 0.00167 ( 4) SS BOND : angle 1.48284 ( 8) covalent geometry : bond 0.00426 ( 6892) covalent geometry : angle 0.61676 ( 9346) *********************** 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 222 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: A 178 TYR cc_start: 0.7855 (m-80) cc_final: 0.7532 (m-80) REVERT: B 109 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: B 178 TYR cc_start: 0.7853 (m-80) cc_final: 0.7540 (m-80) REVERT: C 88 ASP cc_start: 0.7613 (t0) cc_final: 0.7277 (t70) REVERT: E 88 ASP cc_start: 0.7582 (t0) cc_final: 0.7260 (t70) REVERT: E 108 ASP cc_start: 0.8761 (p0) cc_final: 0.8519 (p0) REVERT: F 4 MET cc_start: 0.8417 (mtp) cc_final: 0.8184 (mtp) REVERT: F 105 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6710 (tm-30) outliers start: 25 outliers final: 14 residues processed: 210 average time/residue: 0.2240 time to fit residues: 59.7230 Evaluate side-chains 201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 170 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 77 optimal weight: 0.0970 chunk 64 optimal weight: 0.0050 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.162406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115144 restraints weight = 9045.774| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.67 r_work: 0.3248 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6902 Z= 0.115 Angle : 0.583 6.597 9354 Z= 0.292 Chirality : 0.043 0.153 1036 Planarity : 0.004 0.034 1148 Dihedral : 6.461 56.295 936 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.19 % Allowed : 15.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.31), residues: 840 helix: 2.34 (0.29), residues: 288 sheet: 1.29 (0.36), residues: 216 loop : 0.41 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.008 0.001 HIS B 110 PHE 0.014 0.001 PHE B 43 TYR 0.011 0.001 TYR E 109 ARG 0.006 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 376) hydrogen bonds : angle 4.31415 ( 1074) metal coordination : bond 0.00097 ( 6) SS BOND : bond 0.00486 ( 4) SS BOND : angle 1.50351 ( 8) covalent geometry : bond 0.00253 ( 6892) covalent geometry : angle 0.58172 ( 9346) *********************** 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 217 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: A 170 PHE cc_start: 0.7571 (m-10) cc_final: 0.7283 (m-10) REVERT: A 178 TYR cc_start: 0.7832 (m-80) cc_final: 0.7505 (m-80) REVERT: B 109 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: B 170 PHE cc_start: 0.7602 (m-80) cc_final: 0.7308 (m-10) REVERT: C 41 LYS cc_start: 0.9117 (tptm) cc_final: 0.8908 (tptp) REVERT: C 60 ARG cc_start: 0.8076 (tpp-160) cc_final: 0.7712 (ttm110) REVERT: C 88 ASP cc_start: 0.7584 (t0) cc_final: 0.7365 (t70) REVERT: E 16 GLN cc_start: 0.7478 (tt0) cc_final: 0.6942 (mt0) REVERT: E 41 LYS cc_start: 0.9146 (tptm) cc_final: 0.8929 (tptp) REVERT: E 60 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.7685 (ttm110) REVERT: E 88 ASP cc_start: 0.7651 (t0) cc_final: 0.7428 (t70) REVERT: F 4 MET cc_start: 0.8444 (mtp) cc_final: 0.8231 (mtp) REVERT: F 105 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6666 (tm-30) outliers start: 16 outliers final: 7 residues processed: 208 average time/residue: 0.2051 time to fit residues: 55.2299 Evaluate side-chains 195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 71 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.161445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114000 restraints weight = 9054.460| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.67 r_work: 0.3228 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4134 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= 0.127 Angle : 0.583 6.572 9354 Z= 0.292 Chirality : 0.043 0.152 1036 Planarity : 0.004 0.036 1148 Dihedral : 5.785 53.461 932 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.46 % Allowed : 15.98 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.30), residues: 840 helix: 2.49 (0.29), residues: 288 sheet: 1.24 (0.35), residues: 216 loop : 0.31 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 110 HIS 0.008 0.001 HIS A 110 PHE 0.016 0.001 PHE B 39 TYR 0.012 0.001 TYR E 109 ARG 0.006 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 376) hydrogen bonds : angle 4.23175 ( 1074) metal coordination : bond 0.00121 ( 6) SS BOND : bond 0.00117 ( 4) SS BOND : angle 1.34380 ( 8) covalent geometry : bond 0.00285 ( 6892) covalent geometry : angle 0.58163 ( 9346) *********************** 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 221 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: A 170 PHE cc_start: 0.7597 (m-10) cc_final: 0.7367 (m-10) REVERT: A 178 TYR cc_start: 0.7851 (m-80) cc_final: 0.7537 (m-80) REVERT: B 109 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: B 170 PHE cc_start: 0.7591 (m-80) cc_final: 0.7311 (m-10) REVERT: B 178 TYR cc_start: 0.7839 (m-80) cc_final: 0.7351 (m-80) REVERT: C 41 LYS cc_start: 0.9100 (tptm) cc_final: 0.8861 (tptp) REVERT: C 60 ARG cc_start: 0.8072 (tpp-160) cc_final: 0.7802 (ttm110) REVERT: C 88 ASP cc_start: 0.7536 (t0) cc_final: 0.7317 (t70) REVERT: D 105 GLU cc_start: 0.6642 (tm-30) cc_final: 0.6292 (tm-30) REVERT: E 41 LYS cc_start: 0.9122 (tptm) cc_final: 0.8879 (tptp) REVERT: E 60 ARG cc_start: 0.8198 (tpp-160) cc_final: 0.7872 (ttm110) REVERT: E 88 ASP cc_start: 0.7571 (t0) cc_final: 0.7340 (t70) outliers start: 18 outliers final: 9 residues processed: 212 average time/residue: 0.2216 time to fit residues: 60.4556 Evaluate side-chains 206 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 C residue 89 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.159298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111605 restraints weight = 9014.815| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.60 r_work: 0.3195 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6902 Z= 0.169 Angle : 0.623 6.401 9354 Z= 0.314 Chirality : 0.044 0.151 1036 Planarity : 0.004 0.036 1148 Dihedral : 5.808 52.994 932 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.46 % Allowed : 17.62 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.30), residues: 840 helix: 2.37 (0.29), residues: 288 sheet: 1.07 (0.35), residues: 222 loop : 0.20 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 102 HIS 0.003 0.001 HIS E 52 PHE 0.019 0.001 PHE B 39 TYR 0.012 0.001 TYR D 91 ARG 0.007 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 376) hydrogen bonds : angle 4.33493 ( 1074) metal coordination : bond 0.00207 ( 6) SS BOND : bond 0.00164 ( 4) SS BOND : angle 1.24311 ( 8) covalent geometry : bond 0.00399 ( 6892) covalent geometry : angle 0.62186 ( 9346) *********************** 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 214 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: A 170 PHE cc_start: 0.7636 (m-10) cc_final: 0.7426 (m-10) REVERT: A 178 TYR cc_start: 0.7898 (m-80) cc_final: 0.7575 (m-80) REVERT: B 170 PHE cc_start: 0.7600 (m-80) cc_final: 0.7326 (m-10) REVERT: B 178 TYR cc_start: 0.7879 (m-80) cc_final: 0.7562 (m-80) REVERT: C 41 LYS cc_start: 0.9110 (tptm) cc_final: 0.8903 (tptp) REVERT: C 60 ARG cc_start: 0.8155 (tpp-160) cc_final: 0.7824 (ttm110) REVERT: C 88 ASP cc_start: 0.7485 (t0) cc_final: 0.7264 (t70) REVERT: D 92 ASP cc_start: 0.8790 (t0) cc_final: 0.8552 (t0) REVERT: D 105 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6405 (tm-30) REVERT: E 16 GLN cc_start: 0.7859 (tt0) cc_final: 0.7195 (mt0) REVERT: E 41 LYS cc_start: 0.9129 (tptm) cc_final: 0.8908 (tptp) REVERT: E 60 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7847 (ttm110) REVERT: E 88 ASP cc_start: 0.7607 (t0) cc_final: 0.7338 (t70) outliers start: 18 outliers final: 12 residues processed: 203 average time/residue: 0.2206 time to fit residues: 57.3146 Evaluate side-chains 204 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 C residue 89 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 0.0470 chunk 56 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112329 restraints weight = 9037.627| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.59 r_work: 0.3206 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4266 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= 0.154 Angle : 0.610 6.861 9354 Z= 0.307 Chirality : 0.044 0.151 1036 Planarity : 0.004 0.038 1148 Dihedral : 5.763 52.008 932 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.60 % Allowed : 18.03 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.30), residues: 840 helix: 2.41 (0.29), residues: 288 sheet: 1.10 (0.35), residues: 222 loop : 0.14 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 55 HIS 0.003 0.001 HIS E 52 PHE 0.017 0.001 PHE B 39 TYR 0.010 0.001 TYR B 72 ARG 0.007 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 376) hydrogen bonds : angle 4.29245 ( 1074) metal coordination : bond 0.00177 ( 6) SS BOND : bond 0.00119 ( 4) SS BOND : angle 1.21552 ( 8) covalent geometry : bond 0.00361 ( 6892) covalent geometry : angle 0.60938 ( 9346) *********************** 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 219 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7889 (m-80) cc_final: 0.7563 (m-80) REVERT: B 170 PHE cc_start: 0.7579 (m-80) cc_final: 0.7325 (m-10) REVERT: B 178 TYR cc_start: 0.7861 (m-80) cc_final: 0.7401 (m-80) REVERT: C 41 LYS cc_start: 0.9090 (tptm) cc_final: 0.8889 (tptp) REVERT: C 60 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7834 (ttm110) REVERT: C 88 ASP cc_start: 0.7512 (t0) cc_final: 0.7276 (t70) REVERT: C 104 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8580 (pp) REVERT: D 105 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6459 (tm-30) REVERT: E 16 GLN cc_start: 0.7885 (tt0) cc_final: 0.7001 (mt0) REVERT: E 41 LYS cc_start: 0.9108 (tptm) cc_final: 0.8899 (tptp) REVERT: E 60 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7765 (ttm110) REVERT: E 88 ASP cc_start: 0.7574 (t0) cc_final: 0.7310 (t70) REVERT: F 105 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6399 (tm-30) REVERT: F 107 LYS cc_start: 0.4705 (tptt) cc_final: 0.4484 (tptt) outliers start: 19 outliers final: 15 residues processed: 209 average time/residue: 0.2142 time to fit residues: 56.8762 Evaluate side-chains 211 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 C residue 82 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 104 LEU 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 E residue 84 ILE Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.161259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113687 restraints weight = 9049.654| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.68 r_work: 0.3221 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4407 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= 0.131 Angle : 0.600 7.317 9354 Z= 0.301 Chirality : 0.043 0.150 1036 Planarity : 0.004 0.038 1148 Dihedral : 5.693 49.616 932 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.32 % Allowed : 17.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.30), residues: 840 helix: 2.54 (0.29), residues: 288 sheet: 1.14 (0.36), residues: 222 loop : 0.18 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 55 HIS 0.003 0.001 HIS E 52 PHE 0.015 0.001 PHE A 39 TYR 0.010 0.001 TYR E 109 ARG 0.006 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 376) hydrogen bonds : angle 4.24479 ( 1074) metal coordination : bond 0.00122 ( 6) SS BOND : bond 0.00056 ( 4) SS BOND : angle 1.37232 ( 8) covalent geometry : bond 0.00301 ( 6892) covalent geometry : angle 0.59859 ( 9346) *********************** 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 216 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7854 (m-80) cc_final: 0.7517 (m-80) REVERT: B 170 PHE cc_start: 0.7602 (m-80) cc_final: 0.7354 (m-10) REVERT: C 5 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8248 (mmtp) REVERT: C 41 LYS cc_start: 0.9093 (tptm) cc_final: 0.8874 (tptp) REVERT: C 60 ARG cc_start: 0.8150 (tpp-160) cc_final: 0.7843 (ttm110) REVERT: C 88 ASP cc_start: 0.7471 (t0) cc_final: 0.7237 (t70) REVERT: D 92 ASP cc_start: 0.8679 (t0) cc_final: 0.8471 (t0) REVERT: D 105 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6446 (tm-30) REVERT: E 41 LYS cc_start: 0.9088 (tptm) cc_final: 0.8875 (tptp) REVERT: E 60 ARG cc_start: 0.8194 (tpp-160) cc_final: 0.7704 (ttm110) REVERT: E 88 ASP cc_start: 0.7500 (t0) cc_final: 0.7286 (t70) REVERT: F 105 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6283 (tm-30) outliers start: 17 outliers final: 11 residues processed: 208 average time/residue: 0.2205 time to fit residues: 59.1019 Evaluate side-chains 206 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 89 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 68 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN E 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.160901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113597 restraints weight = 9118.803| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.60 r_work: 0.3218 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4478 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= 0.141 Angle : 0.617 7.672 9354 Z= 0.309 Chirality : 0.043 0.150 1036 Planarity : 0.004 0.038 1148 Dihedral : 5.219 50.235 928 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.31), residues: 840 helix: 2.54 (0.29), residues: 288 sheet: 1.17 (0.36), residues: 222 loop : 0.18 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 55 HIS 0.003 0.001 HIS C 52 PHE 0.016 0.001 PHE B 39 TYR 0.010 0.001 TYR E 96 ARG 0.008 0.000 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 376) hydrogen bonds : angle 4.25012 ( 1074) metal coordination : bond 0.00142 ( 6) SS BOND : bond 0.00289 ( 4) SS BOND : angle 1.51160 ( 8) covalent geometry : bond 0.00329 ( 6892) covalent geometry : angle 0.61539 ( 9346) ********************** 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 209 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.7875 (m-80) cc_final: 0.7552 (m-80) REVERT: B 170 PHE cc_start: 0.7578 (m-80) cc_final: 0.7338 (m-10) REVERT: B 178 TYR cc_start: 0.7884 (m-80) cc_final: 0.7414 (m-80) REVERT: C 5 LYS cc_start: 0.8484 (mmmm) cc_final: 0.8227 (mmtm) REVERT: C 60 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7869 (ttm110) REVERT: D 92 ASP cc_start: 0.8680 (t0) cc_final: 0.8470 (t0) REVERT: D 105 GLU cc_start: 0.6759 (tm-30) cc_final: 0.6456 (tm-30) REVERT: E 60 ARG cc_start: 0.8190 (tpp-160) cc_final: 0.7747 (ttm110) REVERT: E 83 MET cc_start: 0.7038 (mpp) cc_final: 0.6399 (mpp) REVERT: F 79 GLU cc_start: 0.8602 (mp0) cc_final: 0.8389 (mp0) REVERT: F 105 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6495 (tm-30) outliers start: 13 outliers final: 13 residues processed: 201 average time/residue: 0.2204 time to fit residues: 57.6322 Evaluate side-chains 201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 89 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 E residue 82 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS C 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.160782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114101 restraints weight = 8993.941| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.56 r_work: 0.3229 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6902 Z= 0.137 Angle : 0.613 9.888 9354 Z= 0.308 Chirality : 0.043 0.147 1036 Planarity : 0.004 0.038 1148 Dihedral : 5.118 46.381 928 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.78 % Allowed : 18.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.31), residues: 840 helix: 2.56 (0.29), residues: 288 sheet: 1.20 (0.36), residues: 222 loop : 0.18 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 55 HIS 0.011 0.001 HIS A 110 PHE 0.016 0.001 PHE A 39 TYR 0.010 0.001 TYR E 96 ARG 0.008 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 376) hydrogen bonds : angle 4.24268 ( 1074) metal coordination : bond 0.00140 ( 6) SS BOND : bond 0.00189 ( 4) SS BOND : angle 1.40297 ( 8) covalent geometry : bond 0.00319 ( 6892) covalent geometry : angle 0.61238 ( 9346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3473.04 seconds wall clock time: 61 minutes 13.34 seconds (3673.34 seconds total)