Starting phenix.real_space_refine on Fri Dec 8 01:07:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dql_27656/12_2023/8dql_27656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dql_27656/12_2023/8dql_27656.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/8dql_27656/12_2023/8dql_27656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dql_27656/12_2023/8dql_27656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dql_27656/12_2023/8dql_27656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dql_27656/12_2023/8dql_27656.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= 0.004 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 9 5.16 5 C 4188 2.51 5 N 1026 2.21 5 O 1179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 48": "OD1" <-> "OD2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6402 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2134 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2134 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "B" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2134 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Time building chain proxies: 3.84, per 1000 atoms: 0.60 Number of scatterers: 6402 At special positions: 0 Unit cell: (95.7, 90.2, 102.3, 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 9 16.00 O 1179 8.00 N 1026 7.00 C 4188 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: 2.47 Conformation dependent library (CDL) restraints added in 1.3 seconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1506 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 45.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'C' and resid 15 through 34 removed outlier: 3.574A pdb=" N LEU C 19 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.510A pdb=" N LEU C 40 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 182 removed outlier: 3.732A pdb=" N ILE C 164 " --> pdb=" O TYR C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 188 through 211 removed outlier: 4.180A pdb=" N ILE C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 193 " --> pdb=" O TYR C 189 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 removed outlier: 4.122A pdb=" N ILE C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 268 removed outlier: 3.876A pdb=" N TYR C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 34 removed outlier: 3.574A pdb=" N LEU A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.509A pdb=" N LEU A 40 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 182 removed outlier: 3.732A pdb=" N ILE A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 188 through 211 removed outlier: 4.180A pdb=" N ILE A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 removed outlier: 4.122A pdb=" N ILE A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 268 removed outlier: 3.876A pdb=" N TYR A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 34 removed outlier: 3.574A pdb=" N LEU B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.509A pdb=" N LEU B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 182 removed outlier: 3.732A pdb=" N ILE B 164 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 188 through 211 removed outlier: 4.179A pdb=" N ILE B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B 193 " --> pdb=" O TYR B 189 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 removed outlier: 4.122A pdb=" N ILE B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 removed outlier: 3.876A pdb=" N TYR B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 49 removed outlier: 6.740A pdb=" N LYS C 65 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE C 47 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP C 63 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 49 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 61 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 121 removed outlier: 3.674A pdb=" N ALA C 135 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 99 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN C 133 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE C 101 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER C 131 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU C 136 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 49 removed outlier: 6.740A pdb=" N LYS A 65 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 47 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP A 63 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 49 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 61 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 121 removed outlier: 3.675A pdb=" N ALA A 135 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 99 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN A 133 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 101 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER A 131 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 136 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 49 removed outlier: 6.740A pdb=" N LYS B 65 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE B 47 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP B 63 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 49 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 61 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 111 through 121 removed outlier: 3.675A pdb=" N ALA B 135 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 99 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN B 133 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE B 101 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER B 131 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 136 " --> pdb=" O GLU B 147 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 891 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: 1.79 Time building geometry restraints manager: 2.59 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: 2010 1.34 - 1.46: 928 1.46 - 1.57: 3569 1.57 - 1.69: 0 1.69 - 1.80: 15 Bond restraints: 6522 Sorted by residual: bond pdb=" CA ASN B 109 " pdb=" CB ASN B 109 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.04e-01 bond pdb=" CA ASN C 109 " pdb=" CB ASN C 109 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.55e-01 bond pdb=" CA ASN A 109 " pdb=" CB ASN A 109 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.34e-01 bond pdb=" CB ASP C 226 " pdb=" CG ASP C 226 " ideal model delta sigma weight residual 1.516 1.500 0.016 2.50e-02 1.60e+03 4.18e-01 bond pdb=" N ASN B 109 " pdb=" CA ASN B 109 " ideal model delta sigma weight residual 1.457 1.466 -0.008 1.29e-02 6.01e+03 3.98e-01 ... (remaining 6517 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.44: 121 107.44 - 114.07: 3739 114.07 - 120.70: 2760 120.70 - 127.33: 2143 127.33 - 133.95: 39 Bond angle restraints: 8802 Sorted by residual: angle pdb=" C LYS A 108 " pdb=" N ASN A 109 " pdb=" CA ASN A 109 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.61e+00 angle pdb=" C LYS C 108 " pdb=" N ASN C 109 " pdb=" CA ASN C 109 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.55e+00 angle pdb=" C LYS B 108 " pdb=" N ASN B 109 " pdb=" CA ASN B 109 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.50e+00 angle pdb=" CA ASN A 109 " pdb=" CB ASN A 109 " pdb=" CG ASN A 109 " ideal model delta sigma weight residual 112.60 114.50 -1.90 1.00e+00 1.00e+00 3.60e+00 angle pdb=" CA ASN B 109 " pdb=" CB ASN B 109 " pdb=" CG ASN B 109 " ideal model delta sigma weight residual 112.60 114.50 -1.90 1.00e+00 1.00e+00 3.60e+00 ... (remaining 8797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 3472 17.76 - 35.52: 407 35.52 - 53.28: 72 53.28 - 71.04: 9 71.04 - 88.79: 3 Dihedral angle restraints: 3963 sinusoidal: 1653 harmonic: 2310 Sorted by residual: dihedral pdb=" CA ASP A 63 " pdb=" CB ASP A 63 " pdb=" CG ASP A 63 " pdb=" OD1 ASP A 63 " ideal model delta sinusoidal sigma weight residual -30.00 -87.47 57.47 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP B 63 " pdb=" CB ASP B 63 " pdb=" CG ASP B 63 " pdb=" OD1 ASP B 63 " ideal model delta sinusoidal sigma weight residual -30.00 -87.39 57.39 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP C 63 " pdb=" CB ASP C 63 " pdb=" CG ASP C 63 " pdb=" OD1 ASP C 63 " ideal model delta sinusoidal sigma weight residual -30.00 -87.36 57.36 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 3960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 687 0.029 - 0.057: 208 0.057 - 0.086: 68 0.086 - 0.115: 36 0.115 - 0.144: 15 Chirality restraints: 1014 Sorted by residual: chirality pdb=" CA ASN A 109 " pdb=" N ASN A 109 " pdb=" C ASN A 109 " pdb=" CB ASN A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ASN C 109 " pdb=" N ASN C 109 " pdb=" C ASN C 109 " pdb=" CB ASN C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ASN B 109 " pdb=" N ASN B 109 " pdb=" C ASN B 109 " pdb=" CB ASN B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1011 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 108 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C LYS A 108 " -0.020 2.00e-02 2.50e+03 pdb=" O LYS A 108 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN A 109 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 108 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C LYS B 108 " -0.019 2.00e-02 2.50e+03 pdb=" O LYS B 108 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN B 109 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 108 " 0.005 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C LYS C 108 " -0.019 2.00e-02 2.50e+03 pdb=" O LYS C 108 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN C 109 " 0.006 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1923 2.83 - 3.35: 5721 3.35 - 3.86: 9828 3.86 - 4.38: 10992 4.38 - 4.90: 19852 Nonbonded interactions: 48316 Sorted by model distance: nonbonded pdb=" O VAL C 45 " pdb=" OG1 THR C 155 " model vdw 2.309 2.440 nonbonded pdb=" O VAL A 45 " pdb=" OG1 THR A 155 " model vdw 2.309 2.440 nonbonded pdb=" O VAL B 45 " pdb=" OG1 THR B 155 " model vdw 2.309 2.440 nonbonded pdb=" NZ LYS A 104 " pdb=" OE1 GLN A 117 " model vdw 2.340 2.520 nonbonded pdb=" NZ LYS C 104 " pdb=" OE1 GLN C 117 " model vdw 2.341 2.520 ... (remaining 48311 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' selection = chain 'C' } 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: 1.430 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: 6.120 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.700 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.002 0.020 6522 Z= 0.137 Angle : 0.473 5.921 8802 Z= 0.242 Chirality : 0.038 0.144 1014 Planarity : 0.002 0.012 1098 Dihedral : 14.893 88.795 2457 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 2.01 (0.31), residues: 753 helix: 3.77 (0.26), residues: 309 sheet: 2.62 (0.64), residues: 63 loop : -1.12 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 8 HIS 0.002 0.001 HIS C 158 PHE 0.013 0.001 PHE B 2 TYR 0.004 0.001 TYR A 80 ARG 0.003 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.793 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 1.1292 time to fit residues: 106.4835 Evaluate side-chains 72 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.0050 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN B 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6522 Z= 0.159 Angle : 0.529 7.783 8802 Z= 0.274 Chirality : 0.039 0.151 1014 Planarity : 0.003 0.036 1098 Dihedral : 3.361 14.834 843 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.51 % Allowed : 9.19 % Favored : 89.30 % 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: 2.22 (0.32), residues: 753 helix: 4.02 (0.26), residues: 309 sheet: 3.01 (0.68), residues: 63 loop : -1.13 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 8 HIS 0.002 0.001 HIS C 158 PHE 0.022 0.001 PHE C 178 TYR 0.005 0.001 TYR A 35 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.802 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 89 average time/residue: 1.1181 time to fit residues: 105.3504 Evaluate side-chains 73 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.1203 time to fit residues: 1.6453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6522 Z= 0.215 Angle : 0.547 8.261 8802 Z= 0.284 Chirality : 0.040 0.154 1014 Planarity : 0.003 0.036 1098 Dihedral : 3.505 14.860 843 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.74 % Allowed : 11.25 % Favored : 86.01 % 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: 2.02 (0.31), residues: 753 helix: 3.94 (0.27), residues: 309 sheet: 3.06 (0.68), residues: 63 loop : -1.36 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 8 HIS 0.003 0.001 HIS C 158 PHE 0.018 0.001 PHE C 178 TYR 0.008 0.001 TYR B 76 ARG 0.006 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.840 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 84 average time/residue: 0.9823 time to fit residues: 87.9529 Evaluate side-chains 75 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1111 time to fit residues: 1.5742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6522 Z= 0.157 Angle : 0.519 8.868 8802 Z= 0.270 Chirality : 0.039 0.144 1014 Planarity : 0.003 0.038 1098 Dihedral : 3.316 15.872 843 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.47 % Allowed : 12.21 % Favored : 85.32 % 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: 2.01 (0.31), residues: 753 helix: 3.98 (0.27), residues: 309 sheet: 3.12 (0.67), residues: 63 loop : -1.43 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 8 HIS 0.002 0.001 HIS C 158 PHE 0.017 0.001 PHE C 178 TYR 0.007 0.001 TYR A 35 ARG 0.008 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.719 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 83 average time/residue: 0.9803 time to fit residues: 86.8067 Evaluate side-chains 78 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1119 time to fit residues: 1.5773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6522 Z= 0.222 Angle : 0.545 9.201 8802 Z= 0.285 Chirality : 0.040 0.147 1014 Planarity : 0.004 0.043 1098 Dihedral : 3.491 14.839 843 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.88 % Allowed : 13.58 % Favored : 83.54 % 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: 1.84 (0.31), residues: 753 helix: 3.83 (0.27), residues: 309 sheet: 3.05 (0.67), residues: 63 loop : -1.52 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 8 HIS 0.003 0.001 HIS C 158 PHE 0.015 0.001 PHE C 178 TYR 0.008 0.001 TYR A 35 ARG 0.008 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.791 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 89 average time/residue: 0.9795 time to fit residues: 92.9024 Evaluate side-chains 82 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1396 time to fit residues: 1.6138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6522 Z= 0.217 Angle : 0.538 6.509 8802 Z= 0.279 Chirality : 0.040 0.171 1014 Planarity : 0.004 0.047 1098 Dihedral : 3.504 15.065 843 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.61 % Allowed : 14.68 % Favored : 82.72 % 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: 1.77 (0.31), residues: 753 helix: 3.77 (0.27), residues: 309 sheet: 3.09 (0.68), residues: 63 loop : -1.57 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 8 HIS 0.003 0.001 HIS C 158 PHE 0.015 0.001 PHE C 178 TYR 0.009 0.001 TYR A 228 ARG 0.010 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.766 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 84 average time/residue: 1.0258 time to fit residues: 91.6683 Evaluate side-chains 80 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1473 time to fit residues: 1.7515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN B 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6522 Z= 0.154 Angle : 0.504 9.538 8802 Z= 0.262 Chirality : 0.038 0.148 1014 Planarity : 0.003 0.048 1098 Dihedral : 3.339 15.398 843 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.16 % Allowed : 14.40 % Favored : 82.44 % 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: 1.84 (0.32), residues: 753 helix: 3.84 (0.27), residues: 309 sheet: 3.12 (0.67), residues: 63 loop : -1.55 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 8 HIS 0.002 0.001 HIS C 158 PHE 0.015 0.001 PHE C 178 TYR 0.009 0.001 TYR A 228 ARG 0.011 0.001 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.886 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 91 average time/residue: 0.9671 time to fit residues: 94.2532 Evaluate side-chains 78 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.1444 time to fit residues: 1.9505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.0060 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6522 Z= 0.154 Angle : 0.529 8.110 8802 Z= 0.266 Chirality : 0.039 0.185 1014 Planarity : 0.003 0.051 1098 Dihedral : 3.305 15.371 843 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.74 % Allowed : 14.95 % Favored : 82.30 % 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 (0.32), residues: 753 helix: 3.86 (0.27), residues: 309 sheet: 3.07 (0.67), residues: 63 loop : -1.53 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 8 HIS 0.001 0.001 HIS C 158 PHE 0.027 0.001 PHE C 178 TYR 0.010 0.001 TYR A 228 ARG 0.013 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 0.781 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 82 average time/residue: 0.8222 time to fit residues: 72.0796 Evaluate side-chains 78 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.583 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0850 time to fit residues: 0.8976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6522 Z= 0.153 Angle : 0.529 10.190 8802 Z= 0.268 Chirality : 0.039 0.146 1014 Planarity : 0.003 0.030 1098 Dihedral : 3.245 15.190 843 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.47 % Allowed : 15.36 % Favored : 82.17 % 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 (0.32), residues: 753 helix: 3.87 (0.27), residues: 309 sheet: 3.06 (0.67), residues: 63 loop : -1.53 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 8 HIS 0.001 0.001 HIS C 158 PHE 0.025 0.001 PHE C 178 TYR 0.011 0.001 TYR A 228 ARG 0.007 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 1.090 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 83 average time/residue: 1.0629 time to fit residues: 93.7382 Evaluate side-chains 80 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.1082 time to fit residues: 1.3805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.0670 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6522 Z= 0.169 Angle : 0.544 8.466 8802 Z= 0.270 Chirality : 0.039 0.144 1014 Planarity : 0.003 0.057 1098 Dihedral : 3.326 15.159 843 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.92 % Allowed : 16.05 % Favored : 82.03 % 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: 1.84 (0.32), residues: 753 helix: 3.85 (0.27), residues: 309 sheet: 3.04 (0.67), residues: 63 loop : -1.54 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 8 HIS 0.002 0.001 HIS C 158 PHE 0.024 0.001 PHE C 178 TYR 0.016 0.001 TYR A 228 ARG 0.014 0.001 ARG B 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.884 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 1.1530 time to fit residues: 96.6900 Evaluate side-chains 77 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.838 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.0933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105176 restraints weight = 9140.299| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.21 r_work: 0.3163 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6522 Z= 0.211 Angle : 0.581 10.569 8802 Z= 0.292 Chirality : 0.040 0.151 1014 Planarity : 0.003 0.030 1098 Dihedral : 3.422 15.294 843 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.06 % Allowed : 15.78 % Favored : 82.17 % 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: 1.73 (0.31), residues: 753 helix: 3.75 (0.27), residues: 309 sheet: 2.98 (0.68), residues: 63 loop : -1.61 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 8 HIS 0.002 0.001 HIS C 158 PHE 0.023 0.001 PHE C 178 TYR 0.019 0.001 TYR A 228 ARG 0.007 0.001 ARG B 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.71 seconds wall clock time: 43 minutes 35.05 seconds (2615.05 seconds total)