Starting phenix.real_space_refine on Fri Dec 8 02:54:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/12_2023/8t07_40937.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/12_2023/8t07_40937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/12_2023/8t07_40937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/12_2023/8t07_40937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/12_2023/8t07_40937.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/12_2023/8t07_40937.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 44 5.16 5 C 4352 2.51 5 N 1090 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6710 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.06, per 1000 atoms: 0.61 Number of scatterers: 6710 At special positions: 0 Unit cell: (87.15, 110.39, 104.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 44 16.00 O 1222 8.00 N 1090 7.00 C 4352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 44.0% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.586A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 30 through 50 Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.701A pdb=" N CYS A 59 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.620A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 115 through 141 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.513A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 30 through 50 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.702A pdb=" N CYS B 59 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 87 removed outlier: 3.620A pdb=" N LEU B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 115 through 141 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 177 through 195 removed outlier: 3.513A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'F' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.952A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.710A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.952A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.709A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N HIS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1243 1.33 - 1.46: 1814 1.46 - 1.58: 3759 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 6888 Sorted by residual: bond pdb=" C ARG B 93 " pdb=" N SER B 94 " ideal model delta sigma weight residual 1.335 1.423 -0.088 1.30e-02 5.92e+03 4.61e+01 bond pdb=" N ARG C 68 " pdb=" CA ARG C 68 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" N ARG E 68 " pdb=" CA ARG E 68 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" C ALA B 86 " pdb=" N ASP B 87 " ideal model delta sigma weight residual 1.330 1.277 0.053 1.30e-02 5.92e+03 1.69e+01 bond pdb=" N SER D 7 " pdb=" CA SER D 7 " ideal model delta sigma weight residual 1.463 1.488 -0.025 6.90e-03 2.10e+04 1.34e+01 ... (remaining 6883 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.72: 211 106.72 - 113.73: 3670 113.73 - 120.75: 3080 120.75 - 127.77: 2310 127.77 - 134.78: 67 Bond angle restraints: 9338 Sorted by residual: angle pdb=" CA GLY D 66 " pdb=" C GLY D 66 " pdb=" O GLY D 66 " ideal model delta sigma weight residual 122.23 118.61 3.62 6.90e-01 2.10e+00 2.76e+01 angle pdb=" CA GLY F 66 " pdb=" C GLY F 66 " pdb=" O GLY F 66 " ideal model delta sigma weight residual 122.23 118.65 3.58 6.90e-01 2.10e+00 2.69e+01 angle pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" O GLY E 113 " ideal model delta sigma weight residual 122.29 118.11 4.18 8.10e-01 1.52e+00 2.67e+01 angle pdb=" CA GLY C 113 " pdb=" C GLY C 113 " pdb=" O GLY C 113 " ideal model delta sigma weight residual 122.29 118.11 4.18 8.10e-01 1.52e+00 2.66e+01 angle pdb=" C PHE E 54 " pdb=" N TRP E 55 " pdb=" CA TRP E 55 " ideal model delta sigma weight residual 120.38 127.28 -6.90 1.37e+00 5.33e-01 2.54e+01 ... (remaining 9333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 3542 13.92 - 27.85: 371 27.85 - 41.77: 87 41.77 - 55.70: 20 55.70 - 69.62: 14 Dihedral angle restraints: 4034 sinusoidal: 1574 harmonic: 2460 Sorted by residual: dihedral pdb=" CB CYS B 50 " pdb=" SG CYS B 50 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 151.19 -58.19 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 59 " pdb=" CB CYS A 59 " ideal model delta sinusoidal sigma weight residual 93.00 151.16 -58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CA LEU B 58 " pdb=" C LEU B 58 " pdb=" N CYS B 59 " pdb=" CA CYS B 59 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 4031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 395 0.043 - 0.086: 310 0.086 - 0.129: 221 0.129 - 0.172: 90 0.172 - 0.215: 20 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CA ILE F 33 " pdb=" N ILE F 33 " pdb=" C ILE F 33 " pdb=" CB ILE F 33 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE D 33 " pdb=" N ILE D 33 " pdb=" C ILE D 33 " pdb=" CB ILE D 33 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE C 84 " pdb=" N ILE C 84 " pdb=" C ILE C 84 " pdb=" CB ILE C 84 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1033 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 86 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ALA A 86 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA A 86 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP A 87 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 86 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C ALA B 86 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA B 86 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP B 87 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 93 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ARG B 93 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG B 93 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 94 " 0.012 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1664 2.87 - 3.38: 6811 3.38 - 3.89: 11017 3.89 - 4.39: 13006 4.39 - 4.90: 22414 Nonbonded interactions: 54912 Sorted by model distance: nonbonded pdb=" O PRO B 91 " pdb=" OG1 THR B 95 " model vdw 2.368 2.440 nonbonded pdb=" NH2 ARG E 99 " pdb=" OD2 ASP E 108 " model vdw 2.394 2.520 nonbonded pdb=" NH2 ARG C 99 " pdb=" OD2 ASP C 108 " model vdw 2.395 2.520 nonbonded pdb=" O ILE B 104 " pdb=" OG1 THR B 108 " model vdw 2.486 2.440 nonbonded pdb=" O ILE A 104 " pdb=" OG1 THR A 108 " model vdw 2.487 2.440 ... (remaining 54907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 6.050 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 22.980 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.088 6888 Z= 0.887 Angle : 1.710 7.637 9338 Z= 1.277 Chirality : 0.080 0.215 1036 Planarity : 0.004 0.039 1148 Dihedral : 12.725 69.621 2450 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.27 % Allowed : 5.74 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.32 (0.27), residues: 840 helix: -1.20 (0.24), residues: 302 sheet: -0.35 (0.34), residues: 182 loop : -0.63 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 110 HIS 0.007 0.002 HIS A 180 PHE 0.029 0.003 PHE B 46 TYR 0.024 0.003 TYR A 144 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 151 average time/residue: 0.2060 time to fit residues: 40.2434 Evaluate side-chains 116 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4951 time to fit residues: 2.1181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 92 GLN D 30 ASN F 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6888 Z= 0.230 Angle : 0.596 6.415 9338 Z= 0.311 Chirality : 0.042 0.133 1036 Planarity : 0.004 0.034 1148 Dihedral : 4.848 27.178 924 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.09 % Allowed : 11.75 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.40 (0.30), residues: 840 helix: 1.25 (0.29), residues: 302 sheet: -0.50 (0.34), residues: 224 loop : 0.10 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 55 HIS 0.003 0.001 HIS D 49 PHE 0.015 0.002 PHE A 69 TYR 0.015 0.002 TYR A 72 ARG 0.004 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 120 average time/residue: 0.2214 time to fit residues: 34.5869 Evaluate side-chains 118 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0668 time to fit residues: 1.9385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 30 ASN F 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6888 Z= 0.214 Angle : 0.536 6.415 9338 Z= 0.283 Chirality : 0.042 0.220 1036 Planarity : 0.004 0.032 1148 Dihedral : 4.494 24.523 924 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.64 % Allowed : 12.70 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.86 (0.30), residues: 840 helix: 1.75 (0.29), residues: 300 sheet: -0.03 (0.35), residues: 216 loop : 0.02 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 110 HIS 0.003 0.001 HIS C 52 PHE 0.014 0.001 PHE A 39 TYR 0.015 0.001 TYR D 91 ARG 0.002 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 116 average time/residue: 0.2037 time to fit residues: 30.9798 Evaluate side-chains 114 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1387 time to fit residues: 2.1525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 70 optimal weight: 0.0030 chunk 21 optimal weight: 0.8980 overall best weight: 0.9730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6888 Z= 0.230 Angle : 0.534 5.980 9338 Z= 0.280 Chirality : 0.042 0.174 1036 Planarity : 0.004 0.030 1148 Dihedral : 4.329 22.805 924 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.87 % Allowed : 12.57 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.01 (0.30), residues: 840 helix: 1.93 (0.29), residues: 288 sheet: 0.24 (0.36), residues: 216 loop : -0.04 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 110 HIS 0.003 0.001 HIS C 52 PHE 0.014 0.001 PHE A 39 TYR 0.014 0.002 TYR B 72 ARG 0.005 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 123 average time/residue: 0.1883 time to fit residues: 31.0945 Evaluate side-chains 117 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1112 time to fit residues: 2.4606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN D 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6888 Z= 0.172 Angle : 0.514 6.308 9338 Z= 0.263 Chirality : 0.040 0.154 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.103 22.661 924 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.68 % Allowed : 14.07 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.29 (0.30), residues: 840 helix: 2.18 (0.29), residues: 288 sheet: 0.59 (0.36), residues: 220 loop : -0.06 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 110 HIS 0.002 0.001 HIS E 52 PHE 0.013 0.001 PHE A 39 TYR 0.009 0.001 TYR B 72 ARG 0.007 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 113 average time/residue: 0.1922 time to fit residues: 28.9414 Evaluate side-chains 108 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 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 152 GLN B 152 GLN D 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6888 Z= 0.213 Angle : 0.522 6.021 9338 Z= 0.269 Chirality : 0.041 0.130 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.075 21.895 924 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.96 % Allowed : 15.57 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.26 (0.29), residues: 840 helix: 2.17 (0.29), residues: 288 sheet: 0.59 (0.36), residues: 220 loop : -0.12 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 110 HIS 0.002 0.001 HIS D 49 PHE 0.013 0.001 PHE A 39 TYR 0.012 0.001 TYR A 72 ARG 0.006 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 107 average time/residue: 0.2109 time to fit residues: 29.4383 Evaluate side-chains 106 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0492 time to fit residues: 0.9097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6888 Z= 0.289 Angle : 0.555 6.177 9338 Z= 0.288 Chirality : 0.042 0.138 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.304 26.617 924 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.91 % Allowed : 14.34 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.95 (0.29), residues: 840 helix: 1.97 (0.29), residues: 288 sheet: 0.29 (0.35), residues: 216 loop : -0.24 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 110 HIS 0.003 0.001 HIS F 49 PHE 0.015 0.002 PHE A 39 TYR 0.016 0.002 TYR A 72 ARG 0.006 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 114 average time/residue: 0.2088 time to fit residues: 31.2102 Evaluate side-chains 110 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0903 time to fit residues: 1.5293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6888 Z= 0.204 Angle : 0.542 9.062 9338 Z= 0.270 Chirality : 0.041 0.139 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.175 26.175 924 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.50 % Allowed : 15.03 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.10 (0.29), residues: 840 helix: 2.15 (0.29), residues: 288 sheet: 0.38 (0.36), residues: 220 loop : -0.23 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 113 HIS 0.002 0.001 HIS C 52 PHE 0.013 0.001 PHE A 39 TYR 0.011 0.001 TYR B 72 ARG 0.006 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 115 average time/residue: 0.2006 time to fit residues: 30.5087 Evaluate side-chains 112 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0820 time to fit residues: 1.4555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 0.0020 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6888 Z= 0.174 Angle : 0.522 8.858 9338 Z= 0.260 Chirality : 0.040 0.143 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.057 24.896 924 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.23 % Allowed : 15.16 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.25 (0.29), residues: 840 helix: 2.33 (0.29), residues: 288 sheet: 0.50 (0.36), residues: 220 loop : -0.23 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 113 HIS 0.002 0.001 HIS C 52 PHE 0.012 0.001 PHE A 39 TYR 0.010 0.001 TYR A 150 ARG 0.006 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 122 average time/residue: 0.1871 time to fit residues: 30.6206 Evaluate side-chains 111 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0596 time to fit residues: 1.2012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 65 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.0070 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6888 Z= 0.148 Angle : 0.511 8.699 9338 Z= 0.253 Chirality : 0.040 0.144 1036 Planarity : 0.004 0.028 1148 Dihedral : 3.885 23.478 924 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.82 % Allowed : 15.16 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.45 (0.30), residues: 840 helix: 2.53 (0.29), residues: 288 sheet: 0.67 (0.36), residues: 220 loop : -0.19 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 113 HIS 0.002 0.001 HIS E 52 PHE 0.011 0.001 PHE B 39 TYR 0.009 0.001 TYR F 71 ARG 0.006 0.000 ARG E 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 127 average time/residue: 0.1858 time to fit residues: 31.6990 Evaluate side-chains 110 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.195267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163384 restraints weight = 7215.838| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.64 r_work: 0.3743 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6888 Z= 0.164 Angle : 0.525 8.548 9338 Z= 0.260 Chirality : 0.040 0.141 1036 Planarity : 0.004 0.028 1148 Dihedral : 3.895 23.517 924 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.55 % Allowed : 15.44 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.49 (0.30), residues: 840 helix: 2.56 (0.29), residues: 288 sheet: 0.65 (0.36), residues: 220 loop : -0.14 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 49 HIS 0.002 0.001 HIS C 52 PHE 0.012 0.001 PHE B 39 TYR 0.011 0.001 TYR A 150 ARG 0.007 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.00 seconds wall clock time: 36 minutes 22.13 seconds (2182.13 seconds total)