Starting phenix.real_space_refine (version: dev) on Fri Feb 17 13:11:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/02_2023/6hu7_0273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/02_2023/6hu7_0273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/02_2023/6hu7_0273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/02_2023/6hu7_0273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/02_2023/6hu7_0273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/02_2023/6hu7_0273.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.079 sd= 1.306 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 Process input model Symmetric amino acids flipped Residue "B ARG 82": "NH1" <-> "NH2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "D ARG 150": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 4890 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1218 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain: "A" Number of atoms: 1190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 12, 'TRANS': 134} Conformer: "B" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 12, 'TRANS': 134} bond proxies already assigned to first conformer: 1185 Chain: "C" Number of atoms: 1218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1207 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Conformer: "B" Number of residues, atoms: 151, 1207 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} bond proxies already assigned to first conformer: 1230 Chain: "D" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1207 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 127 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 127 " occ=0.50 residue: pdb=" N AARG C 82 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 82 " occ=0.50 Time building chain proxies: 4.20, per 1000 atoms: 0.86 Number of scatterers: 4890 At special positions: 0 Unit cell: (107.712, 117.216, 81.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 888 8.00 N 820 7.00 C 3155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.0 seconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 18 through 19 No H-bonds generated for 'chain 'B' and resid 18 through 19' Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 26 through 43 removed outlier: 3.585A pdb=" N ARG B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.718A pdb=" N GLY B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 110 removed outlier: 3.654A pdb=" N ASP B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.822A pdb=" N PHE A 24 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 49 through 76 removed outlier: 3.545A pdb=" N LEU A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 111 removed outlier: 3.507A pdb=" N ASP A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.588A pdb=" N LEU C 16 " --> pdb=" O THR C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 43 removed outlier: 3.639A pdb=" N ARG C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 76 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.523A pdb=" N LEU C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 111 removed outlier: 3.831A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.573A pdb=" N ARG C 127 " --> pdb=" O GLY C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.760A pdb=" N PHE D 24 " --> pdb=" O SER D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.553A pdb=" N GLY D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.505A pdb=" N ASP D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 109 removed outlier: 4.131A pdb=" N LYS D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.570A pdb=" N THR D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 857 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: 1.17 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1564 1.34 - 1.46: 1067 1.46 - 1.57: 2360 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 5030 Sorted by residual: bond pdb=" CG LEU A 97 " pdb=" CD2 LEU A 97 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CG LEU C 30 " pdb=" CD1 LEU C 30 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" CG LEU D 97 " pdb=" CD2 LEU D 97 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CB GLU B 8 " pdb=" CG GLU B 8 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CB ARG A 98 " pdb=" CG ARG A 98 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.04e+00 ... (remaining 5025 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.26: 216 106.26 - 113.22: 2775 113.22 - 120.17: 1890 120.17 - 127.12: 1911 127.12 - 134.08: 92 Bond angle restraints: 6884 Sorted by residual: angle pdb=" CA TYR A 38 " pdb=" CB TYR A 38 " pdb=" CG TYR A 38 " ideal model delta sigma weight residual 113.90 107.49 6.41 1.80e+00 3.09e-01 1.27e+01 angle pdb=" CA TYR C 132 " pdb=" CB TYR C 132 " pdb=" CG TYR C 132 " ideal model delta sigma weight residual 113.90 108.31 5.59 1.80e+00 3.09e-01 9.65e+00 angle pdb=" CA TYR D 38 " pdb=" CB TYR D 38 " pdb=" CG TYR D 38 " ideal model delta sigma weight residual 113.90 108.53 5.37 1.80e+00 3.09e-01 8.89e+00 angle pdb=" C VAL C 148 " pdb=" N VAL C 149 " pdb=" CA VAL C 149 " ideal model delta sigma weight residual 121.97 126.98 -5.01 1.80e+00 3.09e-01 7.75e+00 angle pdb=" C MET D 1 " pdb=" N ASP D 2 " pdb=" CA ASP D 2 " ideal model delta sigma weight residual 122.46 126.24 -3.78 1.41e+00 5.03e-01 7.20e+00 ... (remaining 6879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 2873 15.70 - 31.39: 92 31.39 - 47.08: 27 47.08 - 62.78: 1 62.78 - 78.47: 5 Dihedral angle restraints: 2998 sinusoidal: 1194 harmonic: 1804 Sorted by residual: dihedral pdb=" CA LEU A 143 " pdb=" C LEU A 143 " pdb=" N PRO A 144 " pdb=" CA PRO A 144 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU D 108 " pdb=" C LEU D 108 " pdb=" N THR D 109 " pdb=" CA THR D 109 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU B 143 " pdb=" C LEU B 143 " pdb=" N PRO B 144 " pdb=" CA PRO B 144 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 537 0.047 - 0.094: 203 0.094 - 0.141: 42 0.141 - 0.187: 7 0.187 - 0.234: 1 Chirality restraints: 790 Sorted by residual: chirality pdb=" CG LEU A 97 " pdb=" CB LEU A 97 " pdb=" CD1 LEU A 97 " pdb=" CD2 LEU A 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA HIS A 47 " pdb=" N HIS A 47 " pdb=" C HIS A 47 " pdb=" CB HIS A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CB THR D 109 " pdb=" CA THR D 109 " pdb=" OG1 THR D 109 " pdb=" CG2 THR D 109 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 787 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 18 " -0.026 2.00e-02 2.50e+03 2.28e-02 9.12e+00 pdb=" CG PHE C 18 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE C 18 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 18 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 18 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 132 " 0.025 2.00e-02 2.50e+03 2.05e-02 8.44e+00 pdb=" CG TYR C 132 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 132 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 132 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 132 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 132 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 132 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 132 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 38 " -0.028 2.00e-02 2.50e+03 1.89e-02 7.11e+00 pdb=" CG TYR A 38 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 38 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 38 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 38 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 38 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 38 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 38 " -0.006 2.00e-02 2.50e+03 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 71 2.68 - 3.24: 4989 3.24 - 3.79: 7768 3.79 - 4.35: 10897 4.35 - 4.90: 17311 Nonbonded interactions: 41036 Sorted by model distance: nonbonded pdb=" NH1 ARG B 150 " pdb=" O LEU C 143 " model vdw 2.130 2.520 nonbonded pdb=" OD1 ASP A 2 " pdb=" N ILE A 3 " model vdw 2.165 2.520 nonbonded pdb=" O THR B 146 " pdb=" OG1 THR B 147 " model vdw 2.273 2.440 nonbonded pdb=" O PHE D 24 " pdb=" NH1 ARG D 98 " model vdw 2.283 2.520 nonbonded pdb=" OD1 ASP A 83 " pdb=" N LEU A 84 " model vdw 2.314 2.520 ... (remaining 41031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) selection = (chain 'B' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) selection = (chain 'C' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) selection = (chain 'D' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3155 2.51 5 N 820 2.21 5 O 888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 12.970 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: 27.080 Check model and map are aligned: 0.080 Process input model: 19.960 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 : 0.008 0.071 5030 Z= 0.520 Angle : 0.781 9.018 6884 Z= 0.411 Chirality : 0.050 0.234 790 Planarity : 0.007 0.060 872 Dihedral : 9.806 78.470 1822 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.69 % Favored : 96.81 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.28), residues: 602 helix: -3.23 (0.16), residues: 405 sheet: None (None), residues: 0 loop : 0.50 (0.43), residues: 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.562 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 1.4787 time to fit residues: 184.7420 Evaluate side-chains 94 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.0570 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS B 57 GLN B 75 ASN B 90 ASN B 104 HIS A 47 HIS A 52 HIS A 57 GLN A 75 ASN A 136 ASN C 52 HIS C 75 ASN D 47 HIS D 52 HIS D 90 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5030 Z= 0.201 Angle : 0.660 9.478 6884 Z= 0.331 Chirality : 0.041 0.236 790 Planarity : 0.006 0.042 872 Dihedral : 5.178 23.213 670 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.34 % Favored : 98.15 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.33), residues: 602 helix: -0.25 (0.24), residues: 412 sheet: None (None), residues: 0 loop : 1.17 (0.46), residues: 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.675 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 107 average time/residue: 1.5113 time to fit residues: 167.0092 Evaluate side-chains 94 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.1383 time to fit residues: 1.9835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.0010 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.5846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5030 Z= 0.170 Angle : 0.584 9.728 6884 Z= 0.286 Chirality : 0.039 0.211 790 Planarity : 0.005 0.039 872 Dihedral : 4.715 20.445 670 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.85 % Favored : 97.65 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.34), residues: 602 helix: 0.96 (0.25), residues: 412 sheet: None (None), residues: 0 loop : 1.29 (0.46), residues: 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.573 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 1.3572 time to fit residues: 132.2076 Evaluate side-chains 84 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.7831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN A 99 GLN A 136 ASN D 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5030 Z= 0.184 Angle : 0.562 9.528 6884 Z= 0.274 Chirality : 0.038 0.198 790 Planarity : 0.005 0.037 872 Dihedral : 4.492 18.418 670 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.85 % Favored : 97.65 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.34), residues: 602 helix: 1.45 (0.25), residues: 413 sheet: None (None), residues: 0 loop : 1.38 (0.47), residues: 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.557 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 1.3414 time to fit residues: 136.1867 Evaluate side-chains 91 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.1102 time to fit residues: 1.9560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 0.0060 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 5030 Z= 0.169 Angle : 0.555 9.389 6884 Z= 0.270 Chirality : 0.038 0.172 790 Planarity : 0.005 0.037 872 Dihedral : 4.374 17.174 670 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.02 % Favored : 97.48 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.34), residues: 602 helix: 1.64 (0.26), residues: 413 sheet: None (None), residues: 0 loop : 1.51 (0.47), residues: 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.548 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 1.4315 time to fit residues: 136.2395 Evaluate side-chains 88 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.0589 time to fit residues: 1.8922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.0670 chunk 57 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 5030 Z= 0.153 Angle : 0.555 9.872 6884 Z= 0.264 Chirality : 0.038 0.164 790 Planarity : 0.005 0.036 872 Dihedral : 4.241 15.729 670 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.35 % Favored : 97.31 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.35), residues: 602 helix: 1.74 (0.26), residues: 417 sheet: None (None), residues: 0 loop : 1.59 (0.47), residues: 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.600 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 1.3527 time to fit residues: 135.9985 Evaluate side-chains 91 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.2969 time to fit residues: 2.2179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.0050 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 5030 Z= 0.156 Angle : 0.541 9.122 6884 Z= 0.261 Chirality : 0.038 0.151 790 Planarity : 0.005 0.035 872 Dihedral : 4.191 14.737 670 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.52 % Favored : 97.14 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.35), residues: 602 helix: 1.83 (0.26), residues: 417 sheet: None (None), residues: 0 loop : 1.64 (0.47), residues: 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.619 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 1.4026 time to fit residues: 141.1897 Evaluate side-chains 91 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.8330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.0270 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 5030 Z= 0.154 Angle : 0.537 9.141 6884 Z= 0.260 Chirality : 0.037 0.133 790 Planarity : 0.005 0.034 872 Dihedral : 4.137 14.109 670 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.86 % Favored : 96.81 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.35), residues: 602 helix: 1.94 (0.26), residues: 411 sheet: None (None), residues: 0 loop : 1.70 (0.47), residues: 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.640 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 1.3915 time to fit residues: 137.0221 Evaluate side-chains 93 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.7190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN D 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 5030 Z= 0.158 Angle : 0.535 9.107 6884 Z= 0.260 Chirality : 0.037 0.133 790 Planarity : 0.004 0.034 872 Dihedral : 4.126 13.999 670 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.52 % Favored : 97.14 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.35), residues: 602 helix: 1.98 (0.26), residues: 411 sheet: None (None), residues: 0 loop : 1.73 (0.47), residues: 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.622 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 94 average time/residue: 1.3425 time to fit residues: 130.9406 Evaluate side-chains 92 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.7830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 28 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.0030 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.0470 overall best weight: 0.1646 ------------------------------------------------------------------------------- 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: 0.8327 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 5030 Z= 0.132 Angle : 0.519 9.015 6884 Z= 0.251 Chirality : 0.036 0.159 790 Planarity : 0.004 0.033 872 Dihedral : 4.015 13.846 670 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.35 % Favored : 97.31 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.35), residues: 602 helix: 2.15 (0.26), residues: 409 sheet: None (None), residues: 0 loop : 1.71 (0.48), residues: 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.569 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 1.3015 time to fit residues: 143.0574 Evaluate side-chains 94 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.606 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.8058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.117949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101978 restraints weight = 14289.735| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.88 r_work: 0.3073 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5030 Z= 0.170 Angle : 0.543 9.012 6884 Z= 0.263 Chirality : 0.038 0.148 790 Planarity : 0.005 0.034 872 Dihedral : 4.066 14.470 670 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.35 % Favored : 97.31 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.35), residues: 602 helix: 2.11 (0.26), residues: 409 sheet: None (None), residues: 0 loop : 1.68 (0.47), residues: 193 =============================================================================== Job complete usr+sys time: 3064.72 seconds wall clock time: 55 minutes 13.41 seconds (3313.41 seconds total)