Starting phenix.real_space_refine on Fri Dec 8 04:04:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/12_2023/8t03_40933_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/12_2023/8t03_40933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/12_2023/8t03_40933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/12_2023/8t03_40933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/12_2023/8t03_40933_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/12_2023/8t03_40933_updated.pdb" } resolution = 2.72 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= 0.002 sd= 0.094 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 44 5.16 5 C 4492 2.51 5 N 1092 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "F PHE 73": "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: 6878 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 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: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.49, per 1000 atoms: 0.65 Number of scatterers: 6878 At special positions: 0 Unit cell: (92.13, 103.75, 103.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 44 16.00 P 2 15.00 O 1246 8.00 N 1092 7.00 C 4492 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=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 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: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 12 sheets defined 37.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 Proline residue: A 11 - end of helix removed outlier: 4.388A pdb=" N LEU A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Proline residue: A 20 - end of helix Processing helix chain 'A' and resid 31 through 51 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 63 through 86 Processing helix chain 'A' and resid 92 through 110 Processing helix chain 'A' and resid 119 through 140 Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.704A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 27 Proline residue: B 11 - end of helix removed outlier: 4.387A pdb=" N LEU B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) Proline residue: B 20 - end of helix Processing helix chain 'B' and resid 31 through 51 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 63 through 86 Processing helix chain 'B' and resid 92 through 110 Processing helix chain 'B' and resid 119 through 140 Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 154 through 169 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.704A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'C' and resid 114 through 116 removed outlier: 6.212A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 47 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.645A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= E, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.289A pdb=" N LYS D 103 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ALA D 13 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU D 105 " --> pdb=" O ALA D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 85 through 90 removed outlier: 6.444A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= H, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.215A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU E 47 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.647A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= K, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.288A pdb=" N LYS F 103 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA F 13 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU F 105 " --> pdb=" O ALA F 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 85 through 90 removed outlier: 6.443A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 918 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: 1.88 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1145 1.33 - 1.45: 1929 1.45 - 1.57: 3908 1.57 - 1.69: 4 1.69 - 1.82: 72 Bond restraints: 7058 Sorted by residual: bond pdb=" N LEU A 55 " pdb=" CA LEU A 55 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.00e-02 1.00e+04 1.37e+01 bond pdb=" N LEU B 55 " pdb=" CA LEU B 55 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.00e-02 1.00e+04 1.33e+01 bond pdb=" N LEU B 10 " pdb=" CA LEU B 10 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.33e+01 bond pdb=" N LEU A 10 " pdb=" CA LEU A 10 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.28e+01 bond pdb=" N ARG E 68 " pdb=" CA ARG E 68 " ideal model delta sigma weight residual 1.454 1.504 -0.050 1.42e-02 4.96e+03 1.24e+01 ... (remaining 7053 not shown) Histogram of bond angle deviations from ideal: 94.81 - 102.87: 50 102.87 - 110.93: 2064 110.93 - 118.98: 4328 118.98 - 127.04: 3029 127.04 - 135.10: 93 Bond angle restraints: 9564 Sorted by residual: angle pdb=" C PHE E 54 " pdb=" N TRP E 55 " pdb=" CA TRP E 55 " ideal model delta sigma weight residual 120.38 127.50 -7.12 1.37e+00 5.33e-01 2.70e+01 angle pdb=" C PHE C 54 " pdb=" N TRP C 55 " pdb=" CA TRP C 55 " ideal model delta sigma weight residual 120.38 127.48 -7.10 1.37e+00 5.33e-01 2.68e+01 angle pdb=" CA GLY C 113 " pdb=" C GLY C 113 " pdb=" O GLY C 113 " ideal model delta sigma weight residual 122.24 117.94 4.30 8.70e-01 1.32e+00 2.44e+01 angle pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" O GLY E 113 " ideal model delta sigma weight residual 122.24 117.97 4.27 8.70e-01 1.32e+00 2.41e+01 angle pdb=" CA GLY D 101 " pdb=" C GLY D 101 " pdb=" O GLY D 101 " ideal model delta sigma weight residual 122.29 118.46 3.83 8.10e-01 1.52e+00 2.24e+01 ... (remaining 9559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 4124 35.87 - 71.74: 116 71.74 - 107.61: 4 107.61 - 143.48: 2 143.48 - 179.35: 4 Dihedral angle restraints: 4250 sinusoidal: 1788 harmonic: 2462 Sorted by residual: dihedral pdb=" CA GLU A 90 " pdb=" C GLU A 90 " pdb=" N PRO A 91 " pdb=" CA PRO A 91 " ideal model delta harmonic sigma weight residual 0.00 38.51 -38.51 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA GLU B 90 " pdb=" C GLU B 90 " pdb=" N PRO B 91 " pdb=" CA PRO B 91 " ideal model delta harmonic sigma weight residual 0.00 38.43 -38.43 0 5.00e+00 4.00e-02 5.91e+01 dihedral pdb=" C1 LBN B 303 " pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O3 LBN B 303 " ideal model delta sinusoidal sigma weight residual 275.40 96.05 179.35 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.970: 1052 0.970 - 1.939: 0 1.939 - 2.909: 0 2.909 - 3.879: 0 3.879 - 4.848: 2 Chirality restraints: 1054 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.48 -4.85 2.00e-01 2.50e+01 5.88e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.48 -4.85 2.00e-01 2.50e+01 5.87e+02 chirality pdb=" CA ILE D 75 " pdb=" N ILE D 75 " pdb=" C ILE D 75 " pdb=" CB ILE D 75 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1051 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN B 303 " -0.038 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C42 LBN B 303 " 0.038 2.00e-02 2.50e+03 pdb=" C5 LBN B 303 " 0.039 2.00e-02 2.50e+03 pdb=" C8 LBN B 303 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 303 " 0.038 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C42 LBN A 303 " -0.038 2.00e-02 2.50e+03 pdb=" C5 LBN A 303 " -0.039 2.00e-02 2.50e+03 pdb=" C8 LBN A 303 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 90 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 91 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.026 5.00e-02 4.00e+02 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 349 2.74 - 3.28: 6652 3.28 - 3.82: 10797 3.82 - 4.36: 14972 4.36 - 4.90: 24915 Nonbonded interactions: 57685 Sorted by model distance: nonbonded pdb=" OD1 ASP D 28 " pdb=" O GLY D 68 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP F 28 " pdb=" O GLY F 68 " model vdw 2.206 3.040 nonbonded pdb=" CE1 TYR D 86 " pdb=" CD1 LEU D 104 " model vdw 2.395 3.760 nonbonded pdb=" CE1 TYR F 86 " pdb=" CD1 LEU F 104 " model vdw 2.397 3.760 nonbonded pdb=" NH2 ARG F 61 " pdb=" OE1 GLU F 79 " model vdw 2.430 2.520 ... (remaining 57680 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.980 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.950 Find NCS groups from input model: 0.370 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 0.050 7058 Z= 0.882 Angle : 1.758 11.254 9564 Z= 1.287 Chirality : 0.227 4.848 1054 Planarity : 0.004 0.051 1156 Dihedral : 17.024 179.354 2666 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.63 % Allowed : 4.90 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -0.46 (0.29), residues: 840 helix: -0.62 (0.26), residues: 294 sheet: 0.45 (0.39), residues: 196 loop : -0.27 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 110 HIS 0.008 0.002 HIS B 110 PHE 0.022 0.003 PHE A 46 TYR 0.027 0.003 TYR F 71 ARG 0.003 0.001 ARG B 168 *********************** 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 138 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.842 Fit side-chains outliers start: 12 outliers final: 2 residues processed: 134 average time/residue: 1.1662 time to fit residues: 165.1911 Evaluate side-chains 96 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.9539 time to fit residues: 5.0451 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.0020 chunk 64 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7058 Z= 0.168 Angle : 0.568 6.263 9564 Z= 0.292 Chirality : 0.042 0.163 1054 Planarity : 0.004 0.032 1156 Dihedral : 13.639 151.586 1136 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.86 % Allowed : 11.04 % Favored : 86.10 % 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: 1.04 (0.30), residues: 840 helix: 1.51 (0.29), residues: 296 sheet: 0.71 (0.35), residues: 230 loop : 0.00 (0.39), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 110 HIS 0.003 0.001 HIS B 184 PHE 0.017 0.002 PHE A 46 TYR 0.013 0.001 TYR D 91 ARG 0.003 0.000 ARG C 68 *********************** 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 135 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 0.784 Fit side-chains outliers start: 21 outliers final: 4 residues processed: 120 average time/residue: 1.2082 time to fit residues: 152.7693 Evaluate side-chains 110 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.0108 time to fit residues: 3.1810 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7058 Z= 0.330 Angle : 0.624 6.920 9564 Z= 0.320 Chirality : 0.045 0.160 1054 Planarity : 0.005 0.032 1156 Dihedral : 13.368 153.002 1136 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.90 % Allowed : 11.04 % Favored : 84.06 % 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: 1.05 (0.30), residues: 840 helix: 1.41 (0.28), residues: 294 sheet: 0.66 (0.34), residues: 240 loop : 0.18 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 110 HIS 0.005 0.001 HIS D 38 PHE 0.019 0.002 PHE B 69 TYR 0.016 0.002 TYR F 91 ARG 0.004 0.001 ARG B 107 *********************** 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 140 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 0.747 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 120 average time/residue: 1.3431 time to fit residues: 169.1695 Evaluate side-chains 117 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 1.1902 time to fit residues: 4.8173 ------------------------------------------------------------------------------- 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: 8.9990 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7058 Z= 0.150 Angle : 0.520 6.253 9564 Z= 0.267 Chirality : 0.041 0.155 1054 Planarity : 0.004 0.040 1156 Dihedral : 11.723 145.248 1136 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.00 % Allowed : 14.17 % Favored : 82.83 % 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: 1.48 (0.29), residues: 840 helix: 1.83 (0.28), residues: 294 sheet: 0.93 (0.34), residues: 240 loop : 0.32 (0.39), residues: 306 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 0.015 0.001 PHE A 39 TYR 0.012 0.001 TYR D 91 ARG 0.003 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.795 Fit side-chains outliers start: 22 outliers final: 6 residues processed: 126 average time/residue: 1.3508 time to fit residues: 179.2381 Evaluate side-chains 113 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 1.0206 time to fit residues: 3.1983 ------------------------------------------------------------------------------- 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: 0.0070 chunk 44 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7058 Z= 0.151 Angle : 0.512 6.273 9564 Z= 0.263 Chirality : 0.041 0.151 1054 Planarity : 0.004 0.045 1156 Dihedral : 11.142 136.308 1136 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.86 % Allowed : 15.12 % Favored : 82.02 % 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: 1.76 (0.30), residues: 840 helix: 2.07 (0.28), residues: 294 sheet: 1.10 (0.35), residues: 240 loop : 0.45 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 110 HIS 0.003 0.001 HIS C 52 PHE 0.016 0.001 PHE B 46 TYR 0.012 0.001 TYR D 91 ARG 0.003 0.000 ARG C 100 *********************** 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 137 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.732 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 127 average time/residue: 1.2916 time to fit residues: 172.4931 Evaluate side-chains 119 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 1.0989 time to fit residues: 5.7543 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN D 30 ASN E 16 GLN F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7058 Z= 0.209 Angle : 0.551 6.468 9564 Z= 0.282 Chirality : 0.042 0.148 1054 Planarity : 0.005 0.049 1156 Dihedral : 11.256 135.779 1136 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.45 % Allowed : 17.17 % Favored : 80.38 % 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: 1.74 (0.30), residues: 840 helix: 1.97 (0.28), residues: 294 sheet: 1.12 (0.35), residues: 240 loop : 0.51 (0.40), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 110 HIS 0.003 0.001 HIS D 38 PHE 0.017 0.002 PHE A 46 TYR 0.013 0.001 TYR F 91 ARG 0.002 0.000 ARG B 107 *********************** 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 129 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.782 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 118 average time/residue: 1.2304 time to fit residues: 152.6720 Evaluate side-chains 112 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.7337 time to fit residues: 2.5993 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7058 Z= 0.170 Angle : 0.525 6.278 9564 Z= 0.268 Chirality : 0.041 0.149 1054 Planarity : 0.004 0.049 1156 Dihedral : 10.850 131.366 1136 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.18 % Allowed : 17.44 % Favored : 80.38 % 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: 1.89 (0.30), residues: 840 helix: 2.06 (0.28), residues: 294 sheet: 1.14 (0.34), residues: 240 loop : 0.68 (0.41), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.002 0.001 HIS E 52 PHE 0.016 0.002 PHE A 39 TYR 0.012 0.001 TYR D 91 ARG 0.002 0.000 ARG E 100 *********************** 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 118 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.796 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 109 average time/residue: 1.2304 time to fit residues: 141.5194 Evaluate side-chains 106 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 1.0139 time to fit residues: 3.1391 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN D 30 ASN D 49 HIS D 93 ASN E 16 GLN F 30 ASN F 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7058 Z= 0.353 Angle : 0.633 6.833 9564 Z= 0.321 Chirality : 0.046 0.157 1054 Planarity : 0.005 0.048 1156 Dihedral : 11.602 137.558 1136 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.86 % Allowed : 17.44 % Favored : 79.70 % 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: 1.57 (0.30), residues: 840 helix: 1.68 (0.29), residues: 292 sheet: 1.02 (0.34), residues: 240 loop : 0.59 (0.41), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 110 HIS 0.005 0.001 HIS F 38 PHE 0.021 0.002 PHE B 69 TYR 0.014 0.002 TYR F 86 ARG 0.004 0.000 ARG A 107 *********************** 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 127 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.853 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 117 average time/residue: 1.3544 time to fit residues: 166.3151 Evaluate side-chains 114 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.8479 time to fit residues: 2.8051 ------------------------------------------------------------------------------- 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: 0.1980 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN D 30 ASN E 16 GLN F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7058 Z= 0.170 Angle : 0.535 6.267 9564 Z= 0.273 Chirality : 0.041 0.177 1054 Planarity : 0.004 0.049 1156 Dihedral : 10.924 135.154 1136 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.50 % Allowed : 18.66 % Favored : 79.84 % 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: 1.74 (0.30), residues: 840 helix: 1.91 (0.29), residues: 294 sheet: 1.03 (0.34), residues: 242 loop : 0.66 (0.41), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.003 0.001 HIS E 52 PHE 0.018 0.002 PHE A 46 TYR 0.012 0.001 TYR F 91 ARG 0.002 0.000 ARG E 100 *********************** 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 115 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.789 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 112 average time/residue: 1.2750 time to fit residues: 150.2917 Evaluate side-chains 105 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0645 time to fit residues: 1.2062 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 0.0370 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7058 Z= 0.132 Angle : 0.509 6.162 9564 Z= 0.260 Chirality : 0.040 0.163 1054 Planarity : 0.004 0.051 1156 Dihedral : 10.307 126.513 1136 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.63 % Allowed : 19.21 % Favored : 79.16 % 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: 1.92 (0.30), residues: 840 helix: 2.16 (0.29), residues: 294 sheet: 1.10 (0.34), residues: 242 loop : 0.67 (0.41), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 110 HIS 0.004 0.001 HIS E 52 PHE 0.017 0.001 PHE B 46 TYR 0.011 0.001 TYR C 96 ARG 0.002 0.000 ARG C 100 ********************** 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 122 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.734 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 1.2450 time to fit residues: 156.0478 Evaluate side-chains 114 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.5757 time to fit residues: 2.3194 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114982 restraints weight = 6913.073| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.19 r_work: 0.3078 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7058 Z= 0.247 Angle : 0.579 6.480 9564 Z= 0.295 Chirality : 0.043 0.172 1054 Planarity : 0.005 0.050 1156 Dihedral : 10.822 132.759 1136 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.23 % Allowed : 19.75 % Favored : 79.02 % 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: 1.71 (0.30), residues: 840 helix: 1.83 (0.29), residues: 296 sheet: 1.20 (0.34), residues: 240 loop : 0.50 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.004 0.001 HIS D 38 PHE 0.020 0.002 PHE A 46 TYR 0.013 0.002 TYR F 91 ARG 0.006 0.000 ARG B 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3241.43 seconds wall clock time: 58 minutes 0.64 seconds (3480.64 seconds total)