Starting phenix.real_space_refine on Mon Mar 11 00:24:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/03_2024/7sau_24957.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/03_2024/7sau_24957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/03_2024/7sau_24957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/03_2024/7sau_24957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/03_2024/7sau_24957.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sau_24957/03_2024/7sau_24957.pdb" } resolution = 3.0 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4140 2.51 5 N 1018 2.21 5 O 1135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 31": "OD1" <-> "OD2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "F TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 51": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6317 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1749 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain: "B" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1731 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "C" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 564 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 572 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "G" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 3.94, per 1000 atoms: 0.62 Number of scatterers: 6317 At special positions: 0 Unit cell: (70.72, 69.056, 134.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1135 8.00 N 1018 7.00 C 4140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.17 Conformation dependent library (CDL) restraints added in 1.2 seconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 76.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 7 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 29 through 68 removed outlier: 3.795A pdb=" N PHE A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 104 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 190 through 219 Proline residue: A 196 - end of helix removed outlier: 3.697A pdb=" N ASN A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 4.738A pdb=" N LEU B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 19 " --> pdb=" O MET B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 66 removed outlier: 3.781A pdb=" N PHE B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 103 removed outlier: 3.567A pdb=" N ALA B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TRP B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 133 through 152 removed outlier: 4.309A pdb=" N GLU B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.537A pdb=" N PHE B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 187' Processing helix chain 'B' and resid 190 through 218 Proline residue: B 196 - end of helix removed outlier: 3.689A pdb=" N HIS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 36 Processing helix chain 'C' and resid 39 through 59 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'D' and resid 9 through 36 Processing helix chain 'D' and resid 39 through 58 removed outlier: 3.623A pdb=" N ILE D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'E' and resid 8 through 36 removed outlier: 3.614A pdb=" N LYS E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE E 14 " --> pdb=" O LYS E 10 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 58 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.517A pdb=" N PHE F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 59 removed outlier: 3.532A pdb=" N MET F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA F 59 " --> pdb=" O PHE F 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.503A pdb=" N PHE G 14 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.727A pdb=" N VAL A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1323 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: 2.04 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1979 1.34 - 1.46: 920 1.46 - 1.57: 3508 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 6455 Sorted by residual: bond pdb=" CB PRO C 74 " pdb=" CG PRO C 74 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.35e+00 bond pdb=" CG1 ILE B 28 " pdb=" CD1 ILE B 28 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.23e+00 bond pdb=" CB VAL A 82 " pdb=" CG1 VAL A 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CB MET A 16 " pdb=" CG MET A 16 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.61e+00 ... (remaining 6450 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.20: 119 106.20 - 113.15: 3494 113.15 - 120.09: 2327 120.09 - 127.03: 2719 127.03 - 133.98: 58 Bond angle restraints: 8717 Sorted by residual: angle pdb=" CA ARG B 120 " pdb=" C ARG B 120 " pdb=" N GLU B 121 " ideal model delta sigma weight residual 116.84 122.70 -5.86 1.71e+00 3.42e-01 1.17e+01 angle pdb=" C MET B 16 " pdb=" N TYR B 17 " pdb=" CA TYR B 17 " ideal model delta sigma weight residual 120.31 115.17 5.14 1.52e+00 4.33e-01 1.14e+01 angle pdb=" N LEU A 128 " pdb=" CA LEU A 128 " pdb=" C LEU A 128 " ideal model delta sigma weight residual 110.80 117.77 -6.97 2.13e+00 2.20e-01 1.07e+01 angle pdb=" CA ARG B 120 " pdb=" C ARG B 120 " pdb=" O ARG B 120 " ideal model delta sigma weight residual 120.51 116.47 4.04 1.43e+00 4.89e-01 7.97e+00 angle pdb=" CB ARG B 76 " pdb=" CG ARG B 76 " pdb=" CD ARG B 76 " ideal model delta sigma weight residual 111.30 117.73 -6.43 2.30e+00 1.89e-01 7.82e+00 ... (remaining 8712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 3427 17.04 - 34.07: 343 34.07 - 51.11: 48 51.11 - 68.15: 14 68.15 - 85.19: 5 Dihedral angle restraints: 3837 sinusoidal: 1542 harmonic: 2295 Sorted by residual: dihedral pdb=" CA GLU A 131 " pdb=" C GLU A 131 " pdb=" N GLY A 132 " pdb=" CA GLY A 132 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TRP D 37 " pdb=" C TRP D 37 " pdb=" N THR D 38 " pdb=" CA THR D 38 " ideal model delta harmonic sigma weight residual 180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TRP F 37 " pdb=" C TRP F 37 " pdb=" N THR F 38 " pdb=" CA THR F 38 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 539 0.029 - 0.058: 304 0.058 - 0.086: 89 0.086 - 0.115: 37 0.115 - 0.144: 5 Chirality restraints: 974 Sorted by residual: chirality pdb=" CA ASP A 211 " pdb=" N ASP A 211 " pdb=" C ASP A 211 " pdb=" CB ASP A 211 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA GLN B 151 " pdb=" N GLN B 151 " pdb=" C GLN B 151 " pdb=" CB GLN B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA PRO A 196 " pdb=" N PRO A 196 " pdb=" C PRO A 196 " pdb=" CB PRO A 196 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 971 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 73 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO G 74 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO G 74 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 74 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 73 " 0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO C 74 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 73 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO E 74 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.025 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 66 2.68 - 3.23: 6309 3.23 - 3.79: 9837 3.79 - 4.34: 13280 4.34 - 4.90: 21807 Nonbonded interactions: 51299 Sorted by model distance: nonbonded pdb=" OH TYR B 58 " pdb=" OE2 GLU B 209 " model vdw 2.122 2.440 nonbonded pdb=" OD2 ASP A 62 " pdb=" OH TYR A 80 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR A 58 " pdb=" OE2 GLU A 209 " model vdw 2.238 2.440 nonbonded pdb=" O ASN B 119 " pdb=" ND2 ASN B 119 " model vdw 2.314 2.520 nonbonded pdb=" OD1 ASN B 125 " pdb=" N TYR B 126 " model vdw 2.359 2.520 ... (remaining 51294 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' and resid 5 through 220) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'E' and resid 6 through 76) selection = (chain 'F' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'G' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) } 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: 1.450 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: 4.010 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 21.310 Find NCS groups from input model: 0.510 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.005 0.077 6455 Z= 0.309 Angle : 0.606 7.370 8717 Z= 0.331 Chirality : 0.040 0.144 974 Planarity : 0.005 0.110 1095 Dihedral : 13.767 85.186 2353 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % 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: 0.64 (0.30), residues: 777 helix: 0.82 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.46 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 75 HIS 0.003 0.001 HIS A 188 PHE 0.012 0.001 PHE G 55 TYR 0.031 0.002 TYR B 17 ARG 0.012 0.001 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.747 Fit side-chains REVERT: A 30 LYS cc_start: 0.7710 (tmmt) cc_final: 0.7429 (ttmm) REVERT: A 38 LYS cc_start: 0.7866 (mmmt) cc_final: 0.7155 (mmtp) REVERT: A 59 GLN cc_start: 0.7322 (mt0) cc_final: 0.6849 (mp10) REVERT: A 84 LYS cc_start: 0.7920 (tttp) cc_final: 0.7515 (ttmp) REVERT: A 118 ASP cc_start: 0.8119 (p0) cc_final: 0.7882 (p0) REVERT: B 34 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6805 (mm-30) REVERT: B 80 TYR cc_start: 0.6974 (m-80) cc_final: 0.6663 (m-10) REVERT: B 85 GLN cc_start: 0.7652 (mt0) cc_final: 0.7330 (mt0) REVERT: B 91 ASN cc_start: 0.7662 (m-40) cc_final: 0.7424 (m-40) REVERT: B 113 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6588 (mtt90) REVERT: B 122 LYS cc_start: 0.7702 (mttp) cc_final: 0.7426 (mtmt) REVERT: B 126 TYR cc_start: 0.8093 (t80) cc_final: 0.7632 (t80) REVERT: B 143 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6410 (mt-10) REVERT: B 149 MET cc_start: 0.7400 (mmp) cc_final: 0.7137 (mpm) REVERT: C 33 LYS cc_start: 0.8531 (tptm) cc_final: 0.8317 (tptp) REVERT: D 38 THR cc_start: 0.8002 (p) cc_final: 0.7799 (m) REVERT: D 43 MET cc_start: 0.8181 (mtp) cc_final: 0.7948 (mtp) REVERT: E 33 LYS cc_start: 0.8641 (tptt) cc_final: 0.8297 (tppt) REVERT: E 41 ASP cc_start: 0.7976 (m-30) cc_final: 0.7751 (m-30) REVERT: F 13 ASN cc_start: 0.7162 (t0) cc_final: 0.6864 (m110) REVERT: F 61 GLU cc_start: 0.7110 (pt0) cc_final: 0.6891 (pt0) REVERT: G 7 ASN cc_start: 0.6154 (m110) cc_final: 0.5764 (m-40) REVERT: G 62 LYS cc_start: 0.5998 (mppt) cc_final: 0.5785 (mttp) REVERT: G 67 TYR cc_start: 0.7524 (m-80) cc_final: 0.7272 (m-80) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 1.3141 time to fit residues: 214.1805 Evaluate side-chains 115 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6455 Z= 0.184 Angle : 0.525 7.502 8717 Z= 0.275 Chirality : 0.037 0.117 974 Planarity : 0.005 0.077 1095 Dihedral : 4.120 19.770 833 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.82 % Allowed : 10.00 % Favored : 88.18 % 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: 1.58 (0.31), residues: 777 helix: 1.62 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.61 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 75 HIS 0.002 0.001 HIS E 36 PHE 0.017 0.001 PHE E 55 TYR 0.012 0.001 TYR B 17 ARG 0.008 0.001 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.746 Fit side-chains REVERT: A 38 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7135 (mmtp) REVERT: A 59 GLN cc_start: 0.7381 (mt0) cc_final: 0.6966 (mp10) REVERT: A 84 LYS cc_start: 0.7889 (tttp) cc_final: 0.7413 (ttmp) REVERT: A 118 ASP cc_start: 0.8052 (p0) cc_final: 0.7848 (p0) REVERT: A 211 ASP cc_start: 0.7493 (p0) cc_final: 0.7220 (p0) REVERT: A 214 SER cc_start: 0.8124 (m) cc_final: 0.7753 (p) REVERT: A 217 GLN cc_start: 0.7949 (tt0) cc_final: 0.7225 (pt0) REVERT: B 34 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6762 (mm-30) REVERT: B 80 TYR cc_start: 0.7118 (m-80) cc_final: 0.6786 (m-10) REVERT: B 85 GLN cc_start: 0.7601 (mt0) cc_final: 0.7375 (mt0) REVERT: B 91 ASN cc_start: 0.7596 (m-40) cc_final: 0.7362 (m-40) REVERT: B 113 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6776 (mtt90) REVERT: B 126 TYR cc_start: 0.8110 (t80) cc_final: 0.7624 (t80) REVERT: B 143 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6433 (mt-10) REVERT: B 149 MET cc_start: 0.7327 (mmp) cc_final: 0.6973 (mpm) REVERT: B 163 LEU cc_start: 0.7221 (mt) cc_final: 0.6954 (mp) REVERT: B 182 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: C 33 LYS cc_start: 0.8436 (tptm) cc_final: 0.8189 (tptp) REVERT: E 25 ILE cc_start: 0.8587 (mm) cc_final: 0.8307 (mt) REVERT: E 33 LYS cc_start: 0.8587 (tptt) cc_final: 0.8351 (tppt) REVERT: F 61 GLU cc_start: 0.7183 (pt0) cc_final: 0.6949 (pt0) REVERT: G 7 ASN cc_start: 0.5952 (m110) cc_final: 0.5636 (m-40) REVERT: G 27 ILE cc_start: 0.8785 (mm) cc_final: 0.8373 (mt) REVERT: G 62 LYS cc_start: 0.6136 (mppt) cc_final: 0.5889 (mttp) REVERT: G 67 TYR cc_start: 0.7491 (m-80) cc_final: 0.7221 (m-80) outliers start: 12 outliers final: 3 residues processed: 136 average time/residue: 1.3161 time to fit residues: 187.0885 Evaluate side-chains 119 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6455 Z= 0.179 Angle : 0.507 7.604 8717 Z= 0.264 Chirality : 0.037 0.115 974 Planarity : 0.004 0.064 1095 Dihedral : 3.998 19.593 833 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.42 % Allowed : 13.33 % Favored : 84.24 % 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: 1.90 (0.31), residues: 777 helix: 1.92 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.75 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 69 HIS 0.002 0.001 HIS E 36 PHE 0.013 0.001 PHE G 55 TYR 0.011 0.001 TYR B 17 ARG 0.010 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.779 Fit side-chains REVERT: A 38 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7184 (mmtp) REVERT: A 48 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7723 (mtt) REVERT: A 59 GLN cc_start: 0.7451 (mt0) cc_final: 0.7001 (mp10) REVERT: A 84 LYS cc_start: 0.7905 (tttp) cc_final: 0.7492 (ttmp) REVERT: A 214 SER cc_start: 0.7993 (m) cc_final: 0.7652 (p) REVERT: A 217 GLN cc_start: 0.8005 (tt0) cc_final: 0.7237 (pt0) REVERT: B 34 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6866 (mm-30) REVERT: B 80 TYR cc_start: 0.7095 (m-80) cc_final: 0.6733 (m-10) REVERT: B 85 GLN cc_start: 0.7581 (mt0) cc_final: 0.7231 (mt0) REVERT: B 113 ARG cc_start: 0.7109 (mtt180) cc_final: 0.6701 (mtt90) REVERT: B 126 TYR cc_start: 0.8096 (t80) cc_final: 0.7668 (t80) REVERT: B 143 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6352 (mt-10) REVERT: B 149 MET cc_start: 0.7367 (mmp) cc_final: 0.7108 (mpm) REVERT: B 162 MET cc_start: 0.7025 (tmm) cc_final: 0.6767 (tmm) REVERT: B 182 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: C 33 LYS cc_start: 0.8400 (tptm) cc_final: 0.8182 (tptp) REVERT: C 62 LYS cc_start: 0.6714 (mtpt) cc_final: 0.6436 (mtmt) REVERT: E 25 ILE cc_start: 0.8676 (mm) cc_final: 0.8417 (mt) REVERT: E 33 LYS cc_start: 0.8573 (tptt) cc_final: 0.8334 (tppt) REVERT: F 61 GLU cc_start: 0.7200 (pt0) cc_final: 0.6937 (pt0) REVERT: G 7 ASN cc_start: 0.5986 (m110) cc_final: 0.5699 (m-40) REVERT: G 41 ASP cc_start: 0.7241 (m-30) cc_final: 0.6929 (m-30) REVERT: G 62 LYS cc_start: 0.6222 (mppt) cc_final: 0.5999 (mttp) outliers start: 16 outliers final: 6 residues processed: 129 average time/residue: 1.3109 time to fit residues: 176.8750 Evaluate side-chains 120 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 90 HIS A 219 ASN B 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6455 Z= 0.199 Angle : 0.517 7.819 8717 Z= 0.268 Chirality : 0.038 0.119 974 Planarity : 0.004 0.056 1095 Dihedral : 3.987 19.664 833 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.18 % Allowed : 14.24 % Favored : 82.58 % 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: 777 helix: 2.02 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.85 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 69 HIS 0.002 0.001 HIS A 188 PHE 0.016 0.001 PHE G 55 TYR 0.011 0.001 TYR E 19 ARG 0.010 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.783 Fit side-chains REVERT: A 38 LYS cc_start: 0.7862 (mmmt) cc_final: 0.7209 (mmtp) REVERT: A 48 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7714 (mtt) REVERT: A 59 GLN cc_start: 0.7443 (mt0) cc_final: 0.7102 (mp-120) REVERT: A 84 LYS cc_start: 0.7876 (tttp) cc_final: 0.7501 (ttmp) REVERT: A 103 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7901 (tp) REVERT: A 118 ASP cc_start: 0.7980 (p0) cc_final: 0.7543 (p0) REVERT: A 214 SER cc_start: 0.8052 (m) cc_final: 0.7723 (p) REVERT: B 34 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6858 (mm-30) REVERT: B 80 TYR cc_start: 0.7077 (m-80) cc_final: 0.6701 (m-10) REVERT: B 113 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6723 (mtt90) REVERT: B 126 TYR cc_start: 0.8104 (t80) cc_final: 0.7723 (t80) REVERT: B 143 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6321 (mt-10) REVERT: B 149 MET cc_start: 0.7313 (mmp) cc_final: 0.7034 (mpm) REVERT: B 182 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: C 33 LYS cc_start: 0.8445 (tptm) cc_final: 0.8235 (tptp) REVERT: C 62 LYS cc_start: 0.6787 (mtpt) cc_final: 0.6550 (mtmt) REVERT: E 10 LYS cc_start: 0.7064 (mtpp) cc_final: 0.6662 (mtmm) REVERT: E 25 ILE cc_start: 0.8679 (mm) cc_final: 0.8428 (mt) REVERT: E 33 LYS cc_start: 0.8601 (tptt) cc_final: 0.8380 (tppt) REVERT: F 61 GLU cc_start: 0.7143 (pt0) cc_final: 0.6868 (pt0) REVERT: G 7 ASN cc_start: 0.5989 (m110) cc_final: 0.5633 (m-40) REVERT: G 27 ILE cc_start: 0.8844 (mm) cc_final: 0.8445 (mt) REVERT: G 41 ASP cc_start: 0.7267 (m-30) cc_final: 0.6926 (m-30) REVERT: G 62 LYS cc_start: 0.6174 (mppt) cc_final: 0.5964 (mttp) outliers start: 21 outliers final: 11 residues processed: 130 average time/residue: 1.2107 time to fit residues: 164.9480 Evaluate side-chains 128 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.0020 chunk 30 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6455 Z= 0.288 Angle : 0.568 8.128 8717 Z= 0.295 Chirality : 0.041 0.149 974 Planarity : 0.004 0.051 1095 Dihedral : 4.191 20.485 833 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.94 % Allowed : 15.61 % Favored : 80.45 % 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: 1.76 (0.30), residues: 777 helix: 1.85 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -0.93 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 69 HIS 0.003 0.001 HIS A 188 PHE 0.025 0.002 PHE G 55 TYR 0.014 0.002 TYR B 17 ARG 0.011 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.754 Fit side-chains REVERT: A 38 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7219 (mmtp) REVERT: A 59 GLN cc_start: 0.7457 (mt0) cc_final: 0.7048 (mp10) REVERT: A 84 LYS cc_start: 0.7877 (tttp) cc_final: 0.7559 (ttmp) REVERT: A 103 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7907 (tp) REVERT: A 164 GLU cc_start: 0.7500 (pt0) cc_final: 0.7193 (pt0) REVERT: A 214 SER cc_start: 0.8060 (m) cc_final: 0.7710 (p) REVERT: B 80 TYR cc_start: 0.7045 (m-80) cc_final: 0.6742 (m-10) REVERT: B 113 ARG cc_start: 0.7070 (mtt180) cc_final: 0.6811 (mtt90) REVERT: B 126 TYR cc_start: 0.8095 (t80) cc_final: 0.7737 (t80) REVERT: B 136 ARG cc_start: 0.7125 (mtp85) cc_final: 0.6867 (ttm110) REVERT: B 182 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: C 62 LYS cc_start: 0.6965 (mtpt) cc_final: 0.6698 (mtmt) REVERT: E 10 LYS cc_start: 0.7062 (mtpp) cc_final: 0.6650 (mtmt) REVERT: E 25 ILE cc_start: 0.8689 (mm) cc_final: 0.8461 (mt) REVERT: E 33 LYS cc_start: 0.8622 (tptt) cc_final: 0.8401 (tppt) REVERT: F 15 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7152 (mt) REVERT: G 27 ILE cc_start: 0.8833 (mm) cc_final: 0.8459 (mt) REVERT: G 62 LYS cc_start: 0.6160 (mppt) cc_final: 0.5882 (mttp) outliers start: 26 outliers final: 12 residues processed: 127 average time/residue: 1.2220 time to fit residues: 162.7843 Evaluate side-chains 127 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6455 Z= 0.190 Angle : 0.514 8.323 8717 Z= 0.268 Chirality : 0.038 0.125 974 Planarity : 0.004 0.049 1095 Dihedral : 4.032 19.478 833 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.18 % Allowed : 16.82 % Favored : 80.00 % 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: 2.06 (0.31), residues: 777 helix: 2.08 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -0.84 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 75 HIS 0.002 0.001 HIS A 188 PHE 0.015 0.001 PHE G 55 TYR 0.011 0.001 TYR E 19 ARG 0.011 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.710 Fit side-chains REVERT: A 38 LYS cc_start: 0.7901 (mmmt) cc_final: 0.6959 (mmtp) REVERT: A 42 ASP cc_start: 0.7453 (m-30) cc_final: 0.6876 (m-30) REVERT: A 59 GLN cc_start: 0.7439 (mt0) cc_final: 0.7045 (mp10) REVERT: A 84 LYS cc_start: 0.7886 (tttp) cc_final: 0.7534 (ttmp) REVERT: A 113 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6983 (mtm-85) REVERT: A 118 ASP cc_start: 0.7954 (p0) cc_final: 0.7505 (p0) REVERT: A 162 MET cc_start: 0.8040 (pp-130) cc_final: 0.7744 (ppp) REVERT: A 164 GLU cc_start: 0.7459 (pt0) cc_final: 0.7031 (pt0) REVERT: A 214 SER cc_start: 0.8067 (m) cc_final: 0.7722 (p) REVERT: B 34 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6752 (mm-30) REVERT: B 80 TYR cc_start: 0.7059 (m-80) cc_final: 0.6819 (m-10) REVERT: B 113 ARG cc_start: 0.7059 (mtt180) cc_final: 0.6626 (mtt90) REVERT: B 126 TYR cc_start: 0.8067 (t80) cc_final: 0.7684 (t80) REVERT: B 136 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6864 (ttm110) REVERT: B 182 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: C 62 LYS cc_start: 0.6931 (mtpt) cc_final: 0.6668 (mtmt) REVERT: E 10 LYS cc_start: 0.7051 (mtpp) cc_final: 0.6650 (mtmt) REVERT: E 25 ILE cc_start: 0.8689 (mm) cc_final: 0.8445 (mt) REVERT: E 33 LYS cc_start: 0.8607 (tptt) cc_final: 0.8381 (tppt) REVERT: F 15 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7006 (mt) REVERT: G 27 ILE cc_start: 0.8821 (mm) cc_final: 0.8452 (mt) REVERT: G 62 LYS cc_start: 0.6129 (mppt) cc_final: 0.5854 (mttp) outliers start: 21 outliers final: 9 residues processed: 131 average time/residue: 1.2281 time to fit residues: 168.7616 Evaluate side-chains 127 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 148 ASN G 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6455 Z= 0.171 Angle : 0.500 8.585 8717 Z= 0.260 Chirality : 0.037 0.119 974 Planarity : 0.004 0.046 1095 Dihedral : 3.930 19.081 833 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.73 % Allowed : 18.33 % Favored : 78.94 % 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: 2.16 (0.31), residues: 777 helix: 2.15 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -0.86 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 75 HIS 0.002 0.001 HIS A 188 PHE 0.020 0.001 PHE E 55 TYR 0.011 0.001 TYR E 19 ARG 0.011 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7213 (mmtp) REVERT: A 59 GLN cc_start: 0.7443 (mt0) cc_final: 0.7062 (mp10) REVERT: A 84 LYS cc_start: 0.7819 (tttp) cc_final: 0.7477 (ttmp) REVERT: A 162 MET cc_start: 0.8020 (pp-130) cc_final: 0.7725 (ppp) REVERT: A 164 GLU cc_start: 0.7442 (pt0) cc_final: 0.6991 (pt0) REVERT: A 214 SER cc_start: 0.8069 (m) cc_final: 0.7729 (p) REVERT: B 34 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6737 (mm-30) REVERT: B 80 TYR cc_start: 0.6992 (m-80) cc_final: 0.6572 (m-80) REVERT: B 91 ASN cc_start: 0.7674 (m-40) cc_final: 0.7465 (m-40) REVERT: B 113 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6665 (mtt90) REVERT: B 126 TYR cc_start: 0.8064 (t80) cc_final: 0.7739 (t80) REVERT: B 136 ARG cc_start: 0.7097 (mtp85) cc_final: 0.6847 (ttm110) REVERT: B 182 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: C 62 LYS cc_start: 0.6910 (mtpt) cc_final: 0.6661 (mtmt) REVERT: E 25 ILE cc_start: 0.8688 (mm) cc_final: 0.8448 (mt) REVERT: E 33 LYS cc_start: 0.8601 (tptt) cc_final: 0.8358 (tppt) REVERT: F 15 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6932 (mt) REVERT: G 27 ILE cc_start: 0.8829 (mm) cc_final: 0.8480 (mt) REVERT: G 62 LYS cc_start: 0.6110 (mppt) cc_final: 0.5839 (mttp) outliers start: 18 outliers final: 11 residues processed: 128 average time/residue: 1.2531 time to fit residues: 168.1943 Evaluate side-chains 127 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 85 GLN B 148 ASN G 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6455 Z= 0.153 Angle : 0.498 8.930 8717 Z= 0.256 Chirality : 0.037 0.121 974 Planarity : 0.004 0.050 1095 Dihedral : 3.839 18.958 833 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.73 % Allowed : 18.64 % Favored : 78.64 % 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: 2.31 (0.31), residues: 777 helix: 2.27 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -0.83 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 75 HIS 0.002 0.001 HIS C 36 PHE 0.015 0.001 PHE E 55 TYR 0.011 0.001 TYR E 19 ARG 0.013 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7144 (mmtp) REVERT: A 59 GLN cc_start: 0.7423 (mt0) cc_final: 0.7034 (mp10) REVERT: A 162 MET cc_start: 0.8051 (pp-130) cc_final: 0.7780 (ppp) REVERT: A 164 GLU cc_start: 0.7399 (pt0) cc_final: 0.6961 (pt0) REVERT: A 214 SER cc_start: 0.8019 (m) cc_final: 0.7674 (p) REVERT: B 34 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6689 (mm-30) REVERT: B 80 TYR cc_start: 0.6908 (m-80) cc_final: 0.6641 (m-80) REVERT: B 113 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6628 (mtt90) REVERT: B 126 TYR cc_start: 0.8043 (t80) cc_final: 0.7705 (t80) REVERT: B 182 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: E 10 LYS cc_start: 0.7002 (mtpp) cc_final: 0.6652 (mtmm) REVERT: E 25 ILE cc_start: 0.8713 (mm) cc_final: 0.8465 (mt) REVERT: E 33 LYS cc_start: 0.8595 (tptt) cc_final: 0.8362 (tppt) REVERT: F 15 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6798 (mt) REVERT: G 27 ILE cc_start: 0.8835 (mm) cc_final: 0.8474 (mt) REVERT: G 41 ASP cc_start: 0.7235 (m-30) cc_final: 0.6889 (m-30) REVERT: G 62 LYS cc_start: 0.6083 (mppt) cc_final: 0.5862 (mttp) outliers start: 18 outliers final: 8 residues processed: 119 average time/residue: 1.3354 time to fit residues: 166.7349 Evaluate side-chains 116 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 85 GLN G 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6455 Z= 0.189 Angle : 0.520 7.994 8717 Z= 0.267 Chirality : 0.038 0.136 974 Planarity : 0.004 0.058 1095 Dihedral : 3.880 18.971 833 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.97 % Allowed : 19.24 % Favored : 78.79 % 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: 2.28 (0.31), residues: 777 helix: 2.23 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -0.80 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 75 HIS 0.002 0.001 HIS G 36 PHE 0.017 0.001 PHE E 55 TYR 0.012 0.001 TYR B 17 ARG 0.015 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7854 (mmmt) cc_final: 0.7207 (mmtp) REVERT: A 59 GLN cc_start: 0.7389 (mt0) cc_final: 0.6997 (mp10) REVERT: A 112 ASN cc_start: 0.6548 (t0) cc_final: 0.5709 (t0) REVERT: A 162 MET cc_start: 0.8012 (pp-130) cc_final: 0.7745 (ppp) REVERT: A 164 GLU cc_start: 0.7372 (pt0) cc_final: 0.6983 (pt0) REVERT: A 214 SER cc_start: 0.8072 (m) cc_final: 0.7713 (p) REVERT: B 34 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6754 (mm-30) REVERT: B 80 TYR cc_start: 0.6917 (m-80) cc_final: 0.6698 (m-80) REVERT: B 113 ARG cc_start: 0.7028 (mtt180) cc_final: 0.6649 (mtt90) REVERT: B 126 TYR cc_start: 0.8024 (t80) cc_final: 0.7715 (t80) REVERT: B 182 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: E 10 LYS cc_start: 0.7039 (mtpp) cc_final: 0.6662 (mtmm) REVERT: E 25 ILE cc_start: 0.8716 (mm) cc_final: 0.8461 (mt) REVERT: E 33 LYS cc_start: 0.8605 (tptt) cc_final: 0.8364 (tppt) REVERT: F 15 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6793 (mt) REVERT: G 27 ILE cc_start: 0.8831 (mm) cc_final: 0.8476 (mt) REVERT: G 41 ASP cc_start: 0.7257 (m-30) cc_final: 0.6927 (m-30) REVERT: G 62 LYS cc_start: 0.6098 (mppt) cc_final: 0.5877 (mttp) outliers start: 13 outliers final: 10 residues processed: 119 average time/residue: 1.2525 time to fit residues: 156.1582 Evaluate side-chains 122 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.0470 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 85 GLN G 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 6455 Z= 0.152 Angle : 0.504 8.854 8717 Z= 0.258 Chirality : 0.037 0.126 974 Planarity : 0.004 0.054 1095 Dihedral : 3.779 18.593 833 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.67 % Allowed : 19.85 % Favored : 78.48 % 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: 2.50 (0.31), residues: 777 helix: 2.46 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.81 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 75 HIS 0.002 0.001 HIS C 36 PHE 0.020 0.001 PHE E 55 TYR 0.013 0.001 TYR A 80 ARG 0.014 0.001 ARG A 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 0.739 Fit side-chains REVERT: A 38 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7183 (mmtp) REVERT: A 42 ASP cc_start: 0.7414 (m-30) cc_final: 0.7071 (m-30) REVERT: A 48 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7541 (mtt) REVERT: A 59 GLN cc_start: 0.7393 (mt0) cc_final: 0.6958 (mp10) REVERT: A 164 GLU cc_start: 0.7343 (pt0) cc_final: 0.6960 (pt0) REVERT: A 214 SER cc_start: 0.8072 (m) cc_final: 0.7721 (p) REVERT: B 34 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6705 (mm-30) REVERT: B 113 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6585 (mtt90) REVERT: B 126 TYR cc_start: 0.7981 (t80) cc_final: 0.7654 (t80) REVERT: B 182 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: E 10 LYS cc_start: 0.6990 (mtpp) cc_final: 0.6613 (mtmm) REVERT: E 25 ILE cc_start: 0.8720 (mm) cc_final: 0.8474 (mt) REVERT: E 33 LYS cc_start: 0.8579 (tptt) cc_final: 0.8351 (tppt) REVERT: F 15 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6711 (mt) REVERT: G 27 ILE cc_start: 0.8828 (mm) cc_final: 0.8472 (mt) REVERT: G 41 ASP cc_start: 0.7294 (m-30) cc_final: 0.6961 (m-30) REVERT: G 62 LYS cc_start: 0.6059 (mppt) cc_final: 0.5814 (mttp) outliers start: 11 outliers final: 7 residues processed: 118 average time/residue: 1.2203 time to fit residues: 151.2110 Evaluate side-chains 118 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 85 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103285 restraints weight = 7189.164| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.74 r_work: 0.2944 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6455 Z= 0.183 Angle : 0.517 8.219 8717 Z= 0.265 Chirality : 0.037 0.123 974 Planarity : 0.004 0.053 1095 Dihedral : 3.800 18.623 833 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.67 % Allowed : 20.15 % Favored : 78.18 % 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: 2.35 (0.31), residues: 777 helix: 2.27 (0.21), residues: 589 sheet: None (None), residues: 0 loop : -0.81 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 75 HIS 0.002 0.001 HIS A 188 PHE 0.019 0.001 PHE E 55 TYR 0.011 0.001 TYR A 80 ARG 0.013 0.001 ARG A 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3083.18 seconds wall clock time: 55 minutes 34.93 seconds (3334.93 seconds total)