Starting phenix.real_space_refine on Sat Apr 6 02:27:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/04_2024/8t06_40936.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/04_2024/8t06_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/04_2024/8t06_40936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/04_2024/8t06_40936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/04_2024/8t06_40936.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t06_40936/04_2024/8t06_40936.pdb" } 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 Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.90, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 2.00 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.85 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: 1.86 Time building geometry restraints manager: 2.25 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: 99.59 - 106.66: 220 106.66 - 113.73: 3620 113.73 - 120.79: 3161 120.79 - 127.86: 2280 127.86 - 134.92: 65 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 2.440 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.511 2.440 nonbonded pdb=" NH2 ARG C 99 " pdb=" OD2 ASP C 108 " model vdw 2.528 2.520 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 2.440 ... (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 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: 1.490 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: 5.880 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.030 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.740 ------------------------------------------------------------------------------- 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 0.049 6892 Z= 0.881 Angle : 1.727 6.607 9346 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 0.786 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: 0.2249 time to fit residues: 66.2191 Evaluate side-chains 201 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6892 Z= 0.204 Angle : 0.623 5.827 9346 Z= 0.322 Chirality : 0.043 0.159 1036 Planarity : 0.004 0.030 1148 Dihedral : 6.779 54.704 940 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.01 % Allowed : 11.48 % 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: 1.13 (0.30), residues: 840 helix: 1.07 (0.29), residues: 302 sheet: 0.78 (0.35), residues: 224 loop : 0.63 (0.40), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 35 HIS 0.003 0.001 HIS B 48 PHE 0.017 0.002 PHE D 73 TYR 0.015 0.001 TYR D 91 ARG 0.002 0.000 ARG A 93 *********************** 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 232 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 210 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7794 (tt0) cc_final: 0.7518 (tt0) REVERT: A 178 TYR cc_start: 0.7064 (m-80) cc_final: 0.6771 (m-80) REVERT: B 67 GLU cc_start: 0.7809 (tt0) cc_final: 0.7520 (tt0) REVERT: B 178 TYR cc_start: 0.7076 (m-80) cc_final: 0.6582 (m-80) REVERT: C 41 LYS cc_start: 0.8844 (tttt) cc_final: 0.8513 (tttp) REVERT: C 55 TRP cc_start: 0.7596 (p90) cc_final: 0.7342 (p90) REVERT: C 70 THR cc_start: 0.7924 (p) cc_final: 0.7712 (p) REVERT: C 99 ARG cc_start: 0.7626 (ttp-170) cc_final: 0.6998 (tmm-80) REVERT: C 102 TRP cc_start: 0.7980 (t60) cc_final: 0.7563 (t-100) REVERT: C 108 ASP cc_start: 0.8103 (p0) cc_final: 0.7334 (p0) REVERT: C 109 TYR cc_start: 0.7992 (m-80) cc_final: 0.7715 (m-80) REVERT: D 31 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7936 (mt-10) REVERT: D 42 LYS cc_start: 0.7999 (mttp) cc_final: 0.7669 (mmtm) REVERT: E 41 LYS cc_start: 0.8799 (tttt) cc_final: 0.8444 (tttp) REVERT: E 58 ASP cc_start: 0.8010 (t70) cc_final: 0.7464 (t0) REVERT: E 99 ARG cc_start: 0.7613 (ttp-170) cc_final: 0.6969 (tmm-80) REVERT: E 102 TRP cc_start: 0.7932 (t60) cc_final: 0.7535 (t-100) REVERT: E 108 ASP cc_start: 0.8098 (p0) cc_final: 0.7328 (p0) REVERT: E 109 TYR cc_start: 0.7982 (m-80) cc_final: 0.7701 (m-80) REVERT: F 31 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7948 (mt-10) REVERT: F 42 LYS cc_start: 0.7992 (mttp) cc_final: 0.7659 (mmtm) REVERT: F 77 ASN cc_start: 0.7917 (m110) cc_final: 0.7600 (p0) outliers start: 22 outliers final: 14 residues processed: 218 average time/residue: 0.2154 time to fit residues: 60.2637 Evaluate side-chains 208 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 91 ASP 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 E residue 18 LEU Chi-restraints excluded: chain E residue 91 ASP 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 0.0570 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN C 16 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6892 Z= 0.311 Angle : 0.629 9.184 9346 Z= 0.320 Chirality : 0.045 0.148 1036 Planarity : 0.004 0.035 1148 Dihedral : 6.694 56.595 936 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.87 % Allowed : 12.70 % Favored : 84.43 % 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: 1.46 (0.30), residues: 840 helix: 1.49 (0.28), residues: 290 sheet: 1.08 (0.36), residues: 218 loop : 0.58 (0.40), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 110 HIS 0.003 0.001 HIS A 110 PHE 0.023 0.002 PHE B 39 TYR 0.016 0.002 TYR D 91 ARG 0.003 0.000 ARG B 63 *********************** 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 230 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 209 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7681 (mmm-85) cc_final: 0.7158 (mmm-85) REVERT: A 67 GLU cc_start: 0.7957 (tt0) cc_final: 0.7531 (tt0) REVERT: A 109 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: A 178 TYR cc_start: 0.7148 (m-80) cc_final: 0.6832 (m-80) REVERT: B 63 ARG cc_start: 0.7689 (mmm-85) cc_final: 0.7345 (mmm-85) REVERT: B 109 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.6530 (m-80) REVERT: B 110 HIS cc_start: 0.7838 (t70) cc_final: 0.7537 (t-170) REVERT: B 178 TYR cc_start: 0.7156 (m-80) cc_final: 0.6844 (m-80) REVERT: C 41 LYS cc_start: 0.8836 (tttt) cc_final: 0.8511 (tttp) REVERT: C 58 ASP cc_start: 0.7846 (t70) cc_final: 0.7438 (t70) REVERT: C 99 ARG cc_start: 0.7556 (ttp-170) cc_final: 0.7034 (tmm-80) REVERT: C 102 TRP cc_start: 0.8101 (t60) cc_final: 0.6803 (t-100) REVERT: C 107 MET cc_start: 0.9061 (ptp) cc_final: 0.8846 (ptp) REVERT: C 108 ASP cc_start: 0.8296 (p0) cc_final: 0.7753 (p0) REVERT: D 31 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7981 (mt-10) REVERT: D 42 LYS cc_start: 0.7709 (mttp) cc_final: 0.7414 (mmtm) REVERT: D 77 ASN cc_start: 0.7948 (m110) cc_final: 0.7569 (p0) REVERT: D 105 GLU cc_start: 0.6784 (tt0) cc_final: 0.6480 (tm-30) REVERT: E 41 LYS cc_start: 0.8748 (tttt) cc_final: 0.8419 (tttp) REVERT: E 58 ASP cc_start: 0.8041 (t70) cc_final: 0.7712 (t70) REVERT: E 83 MET cc_start: 0.7553 (mpp) cc_final: 0.7107 (mpp) REVERT: E 100 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.6081 (ptm160) REVERT: E 102 TRP cc_start: 0.8095 (t60) cc_final: 0.6753 (t-100) REVERT: E 107 MET cc_start: 0.9054 (ptp) cc_final: 0.8841 (ptp) REVERT: F 31 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7960 (mt-10) REVERT: F 42 LYS cc_start: 0.7728 (mttp) cc_final: 0.7427 (mmtm) REVERT: F 77 ASN cc_start: 0.7918 (m110) cc_final: 0.7588 (p0) REVERT: F 105 GLU cc_start: 0.6675 (tm-30) cc_final: 0.6134 (tm-30) outliers start: 21 outliers final: 15 residues processed: 220 average time/residue: 0.2284 time to fit residues: 63.0854 Evaluate side-chains 214 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 91 ASP 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 E residue 91 ASP Chi-restraints excluded: chain E residue 100 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6892 Z= 0.365 Angle : 0.640 6.731 9346 Z= 0.327 Chirality : 0.047 0.164 1036 Planarity : 0.004 0.037 1148 Dihedral : 6.733 59.229 936 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.83 % Allowed : 13.52 % 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: 1.36 (0.30), residues: 840 helix: 1.55 (0.29), residues: 298 sheet: 1.11 (0.35), residues: 218 loop : 0.27 (0.39), residues: 324 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 0.023 0.002 PHE A 39 TYR 0.018 0.002 TYR D 91 ARG 0.003 0.000 ARG C 100 *********************** 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 235 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8002 (tt0) cc_final: 0.7737 (tt0) REVERT: A 178 TYR cc_start: 0.7209 (m-80) cc_final: 0.6906 (m-80) REVERT: B 67 GLU cc_start: 0.7873 (tt0) cc_final: 0.7642 (tt0) REVERT: B 109 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: B 178 TYR cc_start: 0.7197 (m-80) cc_final: 0.6904 (m-80) REVERT: C 41 LYS cc_start: 0.8843 (tttt) cc_final: 0.8498 (tttp) REVERT: C 66 LYS cc_start: 0.8275 (ptpt) cc_final: 0.8041 (ptpt) REVERT: C 88 ASP cc_start: 0.7014 (t0) cc_final: 0.6760 (t70) REVERT: D 42 LYS cc_start: 0.7694 (mttp) cc_final: 0.7417 (mmtm) REVERT: D 77 ASN cc_start: 0.7922 (m110) cc_final: 0.7566 (p0) REVERT: D 105 GLU cc_start: 0.6732 (tt0) cc_final: 0.6508 (tm-30) REVERT: E 22 CYS cc_start: 0.6662 (t) cc_final: 0.6459 (t) REVERT: E 41 LYS cc_start: 0.8759 (tttt) cc_final: 0.8429 (tttp) REVERT: E 58 ASP cc_start: 0.8172 (t70) cc_final: 0.7762 (t70) REVERT: E 66 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7964 (ptpt) REVERT: E 73 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8399 (mtmm) REVERT: E 83 MET cc_start: 0.7411 (mpp) cc_final: 0.7131 (mpp) REVERT: E 88 ASP cc_start: 0.7043 (t0) cc_final: 0.6795 (t70) REVERT: F 42 LYS cc_start: 0.7721 (mttp) cc_final: 0.7443 (mmtm) REVERT: F 77 ASN cc_start: 0.7895 (m110) cc_final: 0.7567 (p0) REVERT: F 105 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6190 (tm-30) outliers start: 28 outliers final: 16 residues processed: 222 average time/residue: 0.2139 time to fit residues: 60.0910 Evaluate side-chains 221 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR 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 C residue 91 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR 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 E residue 73 LYS Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain F residue 5 THR 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 66 optimal weight: 5.9990 chunk 44 optimal weight: 0.0030 chunk 1 optimal weight: 0.0030 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6892 Z= 0.163 Angle : 0.550 6.078 9346 Z= 0.273 Chirality : 0.042 0.152 1036 Planarity : 0.004 0.034 1148 Dihedral : 5.917 55.107 932 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.37 % Allowed : 17.62 % Favored : 81.01 % 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: 2.13 (0.29), residues: 296 sheet: 1.37 (0.35), residues: 216 loop : 0.39 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.007 0.002 HIS B 110 PHE 0.015 0.001 PHE A 43 TYR 0.022 0.001 TYR A 176 ARG 0.004 0.000 ARG B 63 *********************** 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 214 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.7433 (mmm-85) REVERT: A 67 GLU cc_start: 0.7869 (tt0) cc_final: 0.7436 (tt0) REVERT: A 109 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.6028 (m-80) REVERT: A 170 PHE cc_start: 0.7358 (m-10) cc_final: 0.7015 (m-10) REVERT: B 63 ARG cc_start: 0.7649 (mmm-85) cc_final: 0.7434 (mmm-85) REVERT: B 67 GLU cc_start: 0.7753 (tt0) cc_final: 0.7503 (tt0) REVERT: B 109 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: B 170 PHE cc_start: 0.7389 (m-80) cc_final: 0.7065 (m-10) REVERT: B 178 TYR cc_start: 0.7175 (m-80) cc_final: 0.6685 (m-80) REVERT: C 41 LYS cc_start: 0.8739 (tttt) cc_final: 0.8408 (tttp) REVERT: C 66 LYS cc_start: 0.8221 (ptpt) cc_final: 0.8008 (ptpt) REVERT: C 74 ASP cc_start: 0.7800 (t0) cc_final: 0.7595 (t0) REVERT: C 88 ASP cc_start: 0.7111 (t0) cc_final: 0.6873 (t70) REVERT: C 102 TRP cc_start: 0.8179 (t60) cc_final: 0.7701 (t-100) REVERT: D 42 LYS cc_start: 0.7646 (mttp) cc_final: 0.7397 (mmtm) REVERT: D 77 ASN cc_start: 0.7861 (m110) cc_final: 0.7515 (p0) REVERT: E 41 LYS cc_start: 0.8703 (tttt) cc_final: 0.8356 (tttp) REVERT: E 58 ASP cc_start: 0.8066 (t70) cc_final: 0.7698 (t70) REVERT: E 66 LYS cc_start: 0.8175 (ptpt) cc_final: 0.7960 (ptpt) REVERT: E 73 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8433 (mtmm) REVERT: E 83 MET cc_start: 0.7305 (mpp) cc_final: 0.7013 (mpp) REVERT: E 88 ASP cc_start: 0.7043 (t0) cc_final: 0.6799 (t70) REVERT: E 96 TYR cc_start: 0.7833 (m-80) cc_final: 0.7595 (m-80) REVERT: E 102 TRP cc_start: 0.8172 (t60) cc_final: 0.7670 (t-100) REVERT: F 42 LYS cc_start: 0.7610 (mttp) cc_final: 0.7369 (mmtm) REVERT: F 77 ASN cc_start: 0.7856 (m110) cc_final: 0.7516 (p0) outliers start: 10 outliers final: 6 residues processed: 210 average time/residue: 0.2154 time to fit residues: 57.4506 Evaluate side-chains 202 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 73 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6892 Z= 0.232 Angle : 0.584 6.601 9346 Z= 0.293 Chirality : 0.043 0.155 1036 Planarity : 0.004 0.034 1148 Dihedral : 5.883 56.528 932 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.78 % Allowed : 18.58 % 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 (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: 1.89 (0.31), residues: 840 helix: 2.16 (0.29), residues: 296 sheet: 1.46 (0.35), residues: 214 loop : 0.35 (0.40), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 110 HIS 0.003 0.001 HIS C 52 PHE 0.018 0.001 PHE B 39 TYR 0.015 0.001 TYR A 176 ARG 0.004 0.000 ARG B 63 *********************** 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 213 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 0.806 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: 0.7713 (mmm-85) cc_final: 0.7439 (mmm-85) REVERT: A 67 GLU cc_start: 0.7968 (tt0) cc_final: 0.7749 (tt0) REVERT: A 170 PHE cc_start: 0.7364 (m-10) cc_final: 0.7090 (m-10) REVERT: A 178 TYR cc_start: 0.7235 (m-80) cc_final: 0.6913 (m-80) REVERT: B 67 GLU cc_start: 0.7750 (tt0) cc_final: 0.7548 (tt0) REVERT: B 109 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: B 170 PHE cc_start: 0.7403 (m-80) cc_final: 0.7127 (m-10) REVERT: B 178 TYR cc_start: 0.7205 (m-80) cc_final: 0.6879 (m-80) REVERT: C 41 LYS cc_start: 0.8744 (tttt) cc_final: 0.8432 (tttp) REVERT: C 66 LYS cc_start: 0.8221 (ptpt) cc_final: 0.7988 (ptpt) REVERT: C 74 ASP cc_start: 0.7734 (t0) cc_final: 0.7502 (t0) REVERT: D 42 LYS cc_start: 0.7671 (mttp) cc_final: 0.7415 (mmtm) REVERT: D 77 ASN cc_start: 0.7892 (m110) cc_final: 0.7545 (p0) REVERT: E 41 LYS cc_start: 0.8733 (tttt) cc_final: 0.8428 (tttp) REVERT: E 66 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7961 (ptpt) REVERT: E 73 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8474 (mtmm) REVERT: E 88 ASP cc_start: 0.7019 (t0) cc_final: 0.6750 (t70) REVERT: F 42 LYS cc_start: 0.7642 (mttp) cc_final: 0.7392 (mmtm) REVERT: F 77 ASN cc_start: 0.7905 (m110) cc_final: 0.7525 (p0) outliers start: 13 outliers final: 8 residues processed: 208 average time/residue: 0.2278 time to fit residues: 60.0333 Evaluate side-chains 204 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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 73 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 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 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6892 Z= 0.201 Angle : 0.570 6.518 9346 Z= 0.282 Chirality : 0.043 0.154 1036 Planarity : 0.004 0.034 1148 Dihedral : 5.791 56.763 932 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.91 % Allowed : 18.03 % 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: 1.97 (0.31), residues: 840 helix: 2.26 (0.29), residues: 296 sheet: 1.43 (0.33), residues: 230 loop : 0.36 (0.42), residues: 314 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 0.016 0.001 PHE A 39 TYR 0.014 0.001 TYR A 176 ARG 0.006 0.000 ARG B 63 *********************** 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 218 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 0.829 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: 0.7678 (mmm-85) cc_final: 0.7427 (mmm-85) REVERT: A 67 GLU cc_start: 0.7980 (tt0) cc_final: 0.7724 (tt0) REVERT: A 170 PHE cc_start: 0.7350 (m-10) cc_final: 0.7071 (m-10) REVERT: A 178 TYR cc_start: 0.7230 (m-80) cc_final: 0.6896 (m-80) REVERT: B 170 PHE cc_start: 0.7403 (m-80) cc_final: 0.7085 (m-10) REVERT: B 178 TYR cc_start: 0.7202 (m-80) cc_final: 0.6722 (m-80) REVERT: C 41 LYS cc_start: 0.8749 (tttt) cc_final: 0.8443 (tttp) REVERT: C 66 LYS cc_start: 0.8168 (ptpt) cc_final: 0.7881 (ptpt) REVERT: C 74 ASP cc_start: 0.7722 (t0) cc_final: 0.7495 (t0) REVERT: C 102 TRP cc_start: 0.8217 (t60) cc_final: 0.6815 (t-100) REVERT: D 42 LYS cc_start: 0.7658 (mttp) cc_final: 0.7401 (mmtm) REVERT: D 77 ASN cc_start: 0.7922 (m110) cc_final: 0.7547 (p0) REVERT: E 41 LYS cc_start: 0.8738 (tttt) cc_final: 0.8392 (tttp) REVERT: E 66 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7911 (ptpt) REVERT: E 73 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8439 (mtmm) REVERT: E 96 TYR cc_start: 0.7882 (m-80) cc_final: 0.7589 (m-80) REVERT: E 102 TRP cc_start: 0.8187 (t60) cc_final: 0.6772 (t-100) REVERT: F 42 LYS cc_start: 0.7674 (mttp) cc_final: 0.7422 (mmtm) REVERT: F 77 ASN cc_start: 0.7838 (m110) cc_final: 0.7491 (p0) REVERT: F 92 ASP cc_start: 0.8424 (t0) cc_final: 0.8099 (t0) REVERT: F 105 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6035 (tm-30) outliers start: 14 outliers final: 7 residues processed: 211 average time/residue: 0.2120 time to fit residues: 57.0977 Evaluate side-chains 208 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 73 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6892 Z= 0.191 Angle : 0.556 6.964 9346 Z= 0.278 Chirality : 0.042 0.168 1036 Planarity : 0.004 0.034 1148 Dihedral : 5.183 56.318 928 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.91 % Allowed : 18.85 % 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 (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: 1.98 (0.31), residues: 840 helix: 2.29 (0.29), residues: 296 sheet: 1.46 (0.33), residues: 230 loop : 0.32 (0.42), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 55 HIS 0.009 0.001 HIS B 110 PHE 0.015 0.001 PHE B 39 TYR 0.013 0.001 TYR A 176 ARG 0.007 0.000 ARG B 63 *********************** 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 217 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7404 (mmm-85) REVERT: A 67 GLU cc_start: 0.7931 (tt0) cc_final: 0.7676 (tt0) REVERT: A 170 PHE cc_start: 0.7425 (m-10) cc_final: 0.7182 (m-10) REVERT: A 178 TYR cc_start: 0.7227 (m-80) cc_final: 0.6867 (m-80) REVERT: B 113 TRP cc_start: 0.7577 (m100) cc_final: 0.7360 (m100) REVERT: B 170 PHE cc_start: 0.7382 (m-80) cc_final: 0.7121 (m-10) REVERT: B 178 TYR cc_start: 0.7203 (m-80) cc_final: 0.6721 (m-80) REVERT: C 39 ILE cc_start: 0.8703 (mt) cc_final: 0.8450 (tt) REVERT: C 41 LYS cc_start: 0.8742 (tttt) cc_final: 0.8442 (tttp) REVERT: C 66 LYS cc_start: 0.8164 (ptpt) cc_final: 0.7872 (ptpt) REVERT: C 74 ASP cc_start: 0.7783 (t0) cc_final: 0.7548 (t0) REVERT: C 102 TRP cc_start: 0.8253 (t60) cc_final: 0.6875 (t-100) REVERT: D 42 LYS cc_start: 0.7661 (mttp) cc_final: 0.7400 (mmtm) REVERT: D 77 ASN cc_start: 0.7964 (m110) cc_final: 0.7602 (p0) REVERT: E 39 ILE cc_start: 0.8699 (mt) cc_final: 0.8428 (tt) REVERT: E 41 LYS cc_start: 0.8763 (tttt) cc_final: 0.8438 (tttp) REVERT: E 66 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7911 (ptpt) REVERT: E 96 TYR cc_start: 0.7861 (m-80) cc_final: 0.7516 (m-80) REVERT: E 102 TRP cc_start: 0.8199 (t60) cc_final: 0.6811 (t-100) REVERT: F 42 LYS cc_start: 0.7668 (mttp) cc_final: 0.7410 (mmtm) REVERT: F 77 ASN cc_start: 0.7900 (m110) cc_final: 0.7545 (p0) REVERT: F 92 ASP cc_start: 0.8434 (t0) cc_final: 0.8108 (t0) REVERT: F 105 GLU cc_start: 0.6584 (tm-30) cc_final: 0.5953 (tm-30) outliers start: 14 outliers final: 10 residues processed: 209 average time/residue: 0.2116 time to fit residues: 56.5605 Evaluate side-chains 210 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 200 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 82 LEU 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 F residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6892 Z= 0.229 Angle : 0.584 7.257 9346 Z= 0.292 Chirality : 0.043 0.184 1036 Planarity : 0.004 0.035 1148 Dihedral : 5.330 57.061 928 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.50 % Allowed : 19.81 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.31), residues: 840 helix: 2.25 (0.29), residues: 296 sheet: 1.50 (0.33), residues: 230 loop : 0.27 (0.41), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 55 HIS 0.003 0.001 HIS C 52 PHE 0.017 0.001 PHE B 39 TYR 0.012 0.001 TYR A 176 ARG 0.006 0.000 ARG B 63 *********************** 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 221 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 210 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7436 (mmm-85) REVERT: A 67 GLU cc_start: 0.7940 (tt0) cc_final: 0.7676 (tt0) REVERT: A 170 PHE cc_start: 0.7401 (m-10) cc_final: 0.7134 (m-10) REVERT: A 178 TYR cc_start: 0.7246 (m-80) cc_final: 0.6912 (m-80) REVERT: B 170 PHE cc_start: 0.7371 (m-80) cc_final: 0.7080 (m-10) REVERT: B 178 TYR cc_start: 0.7220 (m-80) cc_final: 0.6879 (m-80) REVERT: C 22 CYS cc_start: 0.6834 (t) cc_final: 0.6595 (t) REVERT: C 41 LYS cc_start: 0.8724 (tttt) cc_final: 0.8441 (tttp) REVERT: C 66 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7869 (ptpt) REVERT: C 74 ASP cc_start: 0.7796 (t0) cc_final: 0.7562 (t0) REVERT: D 3 GLN cc_start: 0.7866 (mp10) cc_final: 0.7542 (mp10) REVERT: D 42 LYS cc_start: 0.7688 (mttp) cc_final: 0.7424 (mmtm) REVERT: D 77 ASN cc_start: 0.7957 (m110) cc_final: 0.7600 (p0) REVERT: D 92 ASP cc_start: 0.8500 (t0) cc_final: 0.8196 (t0) REVERT: E 41 LYS cc_start: 0.8729 (tttt) cc_final: 0.8432 (tttp) REVERT: E 66 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7855 (ptpt) REVERT: F 42 LYS cc_start: 0.7691 (mttp) cc_final: 0.7424 (mmtm) REVERT: F 77 ASN cc_start: 0.7887 (m110) cc_final: 0.7544 (p0) REVERT: F 92 ASP cc_start: 0.8469 (t0) cc_final: 0.8134 (t0) REVERT: F 105 GLU cc_start: 0.6553 (tm-30) cc_final: 0.5961 (tm-30) outliers start: 11 outliers final: 8 residues processed: 214 average time/residue: 0.2223 time to fit residues: 60.3699 Evaluate side-chains 211 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6892 Z= 0.181 Angle : 0.555 5.950 9346 Z= 0.280 Chirality : 0.043 0.204 1036 Planarity : 0.004 0.034 1148 Dihedral : 5.361 56.025 928 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.09 % Allowed : 20.22 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.03 (0.31), residues: 840 helix: 2.36 (0.29), residues: 296 sheet: 1.52 (0.34), residues: 230 loop : 0.27 (0.41), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 55 HIS 0.003 0.001 HIS C 105 PHE 0.015 0.001 PHE B 39 TYR 0.012 0.001 TYR A 176 ARG 0.006 0.000 ARG B 63 ********************** 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 214 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 0.794 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: 0.7626 (mmm-85) cc_final: 0.7362 (mmm-85) REVERT: A 67 GLU cc_start: 0.7914 (tt0) cc_final: 0.7629 (tt0) REVERT: A 170 PHE cc_start: 0.7411 (m-10) cc_final: 0.7195 (m-10) REVERT: B 170 PHE cc_start: 0.7414 (m-80) cc_final: 0.7162 (m-10) REVERT: B 178 TYR cc_start: 0.7197 (m-80) cc_final: 0.6746 (m-80) REVERT: C 22 CYS cc_start: 0.6838 (t) cc_final: 0.6619 (t) REVERT: C 39 ILE cc_start: 0.8670 (mt) cc_final: 0.8402 (tt) REVERT: C 41 LYS cc_start: 0.8715 (tttt) cc_final: 0.8323 (tptp) REVERT: C 66 LYS cc_start: 0.8119 (ptpt) cc_final: 0.7830 (ptpt) REVERT: D 42 LYS cc_start: 0.7713 (mttp) cc_final: 0.7453 (mmtm) REVERT: D 77 ASN cc_start: 0.7945 (m110) cc_final: 0.7599 (p0) REVERT: D 92 ASP cc_start: 0.8405 (t0) cc_final: 0.8125 (t0) REVERT: D 105 GLU cc_start: 0.6563 (tm-30) cc_final: 0.5901 (tm-30) REVERT: E 41 LYS cc_start: 0.8699 (tttt) cc_final: 0.8384 (tttp) REVERT: E 66 LYS cc_start: 0.8213 (ptpt) cc_final: 0.7975 (ptpt) REVERT: E 74 ASP cc_start: 0.7665 (t0) cc_final: 0.7417 (t0) REVERT: E 96 TYR cc_start: 0.7868 (m-80) cc_final: 0.7514 (m-80) REVERT: E 102 TRP cc_start: 0.8228 (t60) cc_final: 0.7700 (t-100) REVERT: F 42 LYS cc_start: 0.7704 (mttp) cc_final: 0.7451 (mmtm) REVERT: F 77 ASN cc_start: 0.7885 (m110) cc_final: 0.7552 (p0) REVERT: F 92 ASP cc_start: 0.8421 (t0) cc_final: 0.8153 (t0) REVERT: F 105 GLU cc_start: 0.6497 (tm-30) cc_final: 0.5908 (tm-30) outliers start: 8 outliers final: 8 residues processed: 210 average time/residue: 0.2295 time to fit residues: 61.1233 Evaluate side-chains 212 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 204 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 59 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.160494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118662 restraints weight = 8892.415| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.56 r_work: 0.3179 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6892 Z= 0.195 Angle : 0.576 7.423 9346 Z= 0.288 Chirality : 0.043 0.207 1036 Planarity : 0.004 0.034 1148 Dihedral : 5.366 55.944 928 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.50 % Allowed : 20.08 % Favored : 78.42 % 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: 1.98 (0.31), residues: 840 helix: 2.38 (0.29), residues: 296 sheet: 1.36 (0.34), residues: 236 loop : 0.26 (0.41), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 113 HIS 0.009 0.001 HIS B 110 PHE 0.015 0.001 PHE B 39 TYR 0.012 0.001 TYR A 176 ARG 0.006 0.000 ARG B 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.89 seconds wall clock time: 37 minutes 57.04 seconds (2277.04 seconds total)