Starting phenix.real_space_refine on Sat Aug 3 01:56:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuz_43545/08_2024/8vuz_43545.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuz_43545/08_2024/8vuz_43545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuz_43545/08_2024/8vuz_43545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuz_43545/08_2024/8vuz_43545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuz_43545/08_2024/8vuz_43545.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuz_43545/08_2024/8vuz_43545.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4166 2.51 5 N 1114 2.21 5 O 1323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 170": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6626 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1652 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1696 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1590 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Time building chain proxies: 4.22, per 1000 atoms: 0.64 Number of scatterers: 6626 At special positions: 0 Unit cell: (59.76, 67.23, 158.53, 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 23 16.00 O 1323 8.00 N 1114 7.00 C 4166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 141 " - pdb=" SG CYS H 197 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 20 sheets defined 7.0% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.629A pdb=" N GLU A 64 " --> pdb=" O GLN A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.762A pdb=" N SER A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.868A pdb=" N LEU B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.778A pdb=" N THR B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.663A pdb=" N LYS H 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 98 through 100B removed outlier: 3.639A pdb=" N GLY H 100A" --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 193 removed outlier: 3.954A pdb=" N THR H 192 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.911A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.616A pdb=" N VAL A 18 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.282A pdb=" N GLU A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.536A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 177 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 144 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A 175 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.536A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 177 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 144 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A 175 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 154 removed outlier: 7.007A pdb=" N VAL A 193 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 210 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 195 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.741A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.606A pdb=" N GLY B 84 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 37 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.990A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 134 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 178 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.990A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 139 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.720A pdb=" N ASN B 145 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 193 " --> pdb=" O LYS B 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.705A pdb=" N TRP H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 120 through 123 removed outlier: 5.968A pdb=" N TYR H 177 " --> pdb=" O ASP H 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 138 through 139 Processing sheet with id=AB7, first strand: chain 'H' and resid 152 through 155 Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 14 removed outlier: 7.148A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.082A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.666A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 630 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: 1.81 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.95: 1 0.95 - 1.20: 0 1.20 - 1.45: 3014 1.45 - 1.70: 3736 1.70 - 1.95: 29 Bond restraints: 6780 Sorted by residual: bond pdb=" CG PRO L 119 " pdb=" CD PRO L 119 " ideal model delta sigma weight residual 1.503 0.703 0.800 3.40e-02 8.65e+02 5.53e+02 bond pdb=" CB PRO L 119 " pdb=" CG PRO L 119 " ideal model delta sigma weight residual 1.492 1.947 -0.455 5.00e-02 4.00e+02 8.28e+01 bond pdb=" N PRO L 119 " pdb=" CD PRO L 119 " ideal model delta sigma weight residual 1.473 1.599 -0.126 1.40e-02 5.10e+03 8.08e+01 bond pdb=" N PRO L 119 " pdb=" CA PRO L 119 " ideal model delta sigma weight residual 1.465 1.322 0.143 2.03e-02 2.43e+03 4.93e+01 bond pdb=" CB PRO H 214 " pdb=" CG PRO H 214 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.87e+00 ... (remaining 6775 not shown) Histogram of bond angle deviations from ideal: 77.15 - 88.55: 3 88.55 - 99.94: 4 99.94 - 111.33: 3166 111.33 - 122.72: 5041 122.72 - 134.11: 1021 Bond angle restraints: 9235 Sorted by residual: angle pdb=" N PRO L 119 " pdb=" CD PRO L 119 " pdb=" CG PRO L 119 " ideal model delta sigma weight residual 103.20 77.15 26.05 1.50e+00 4.44e-01 3.01e+02 angle pdb=" CA PRO L 119 " pdb=" CB PRO L 119 " pdb=" CG PRO L 119 " ideal model delta sigma weight residual 104.50 83.94 20.56 1.90e+00 2.77e-01 1.17e+02 angle pdb=" CA PRO L 119 " pdb=" N PRO L 119 " pdb=" CD PRO L 119 " ideal model delta sigma weight residual 112.00 96.85 15.15 1.40e+00 5.10e-01 1.17e+02 angle pdb=" N PRO L 119 " pdb=" CA PRO L 119 " pdb=" CB PRO L 119 " ideal model delta sigma weight residual 103.08 95.32 7.76 9.70e-01 1.06e+00 6.40e+01 angle pdb=" CB PRO L 119 " pdb=" CG PRO L 119 " pdb=" CD PRO L 119 " ideal model delta sigma weight residual 106.10 83.74 22.36 3.20e+00 9.77e-02 4.88e+01 ... (remaining 9230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3424 17.78 - 35.56: 505 35.56 - 53.33: 111 53.33 - 71.11: 18 71.11 - 88.89: 10 Dihedral angle restraints: 4068 sinusoidal: 1545 harmonic: 2523 Sorted by residual: dihedral pdb=" CB CYS H 141 " pdb=" SG CYS H 141 " pdb=" SG CYS H 197 " pdb=" CB CYS H 197 " ideal model delta sinusoidal sigma weight residual 93.00 162.64 -69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CA LYS B 50 " pdb=" C LYS B 50 " pdb=" N VAL B 51 " pdb=" CA VAL B 51 " ideal model delta harmonic sigma weight residual -180.00 -144.17 -35.83 0 5.00e+00 4.00e-02 5.13e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 195 " pdb=" CB CYS A 195 " ideal model delta sinusoidal sigma weight residual 93.00 145.51 -52.51 1 1.00e+01 1.00e-02 3.76e+01 ... (remaining 4065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 808 0.045 - 0.090: 171 0.090 - 0.135: 79 0.135 - 0.180: 0 0.180 - 0.224: 1 Chirality restraints: 1059 Sorted by residual: chirality pdb=" CA PRO L 119 " pdb=" N PRO L 119 " pdb=" C PRO L 119 " pdb=" CB PRO L 119 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA PRO B 141 " pdb=" N PRO B 141 " pdb=" C PRO B 141 " pdb=" CB PRO B 141 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA TYR B 140 " pdb=" N TYR B 140 " pdb=" C TYR B 140 " pdb=" CB TYR B 140 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1056 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE L 118 " -0.097 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO L 119 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO L 119 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO L 119 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 213 " -0.093 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO H 214 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO H 214 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO H 214 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO L 59 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.022 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 108 2.62 - 3.19: 5850 3.19 - 3.76: 10027 3.76 - 4.33: 13368 4.33 - 4.90: 22129 Nonbonded interactions: 51482 Sorted by model distance: nonbonded pdb=" OG1 THR B 182 " pdb=" OD1 ASP B 184 " model vdw 2.050 3.040 nonbonded pdb=" OE1 GLN L 166 " pdb=" OG SER L 171 " model vdw 2.140 3.040 nonbonded pdb=" OG SER B 201 " pdb=" O SER B 203 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN A 52 " pdb=" OH TYR L 32 " model vdw 2.234 3.040 nonbonded pdb=" N GLU H 149 " pdb=" OE1 GLU H 149 " model vdw 2.240 3.120 ... (remaining 51477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.710 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.090 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.012 0.800 6780 Z= 0.886 Angle : 0.809 26.045 9235 Z= 0.433 Chirality : 0.044 0.224 1059 Planarity : 0.007 0.135 1175 Dihedral : 17.378 88.887 2422 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.13 % Rotamer: Outliers : 0.13 % Allowed : 35.97 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.21 (0.30), residues: 859 helix: -1.40 (0.75), residues: 36 sheet: 0.44 (0.26), residues: 407 loop : -0.55 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 148 HIS 0.005 0.001 HIS B 198 PHE 0.013 0.002 PHE L 118 TYR 0.020 0.001 TYR L 140 ARG 0.004 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8321 (mppt) cc_final: 0.7921 (mmpt) REVERT: B 149 LYS cc_start: 0.7403 (tttm) cc_final: 0.6937 (tptp) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1804 time to fit residues: 36.2894 Evaluate side-chains 147 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6780 Z= 0.231 Angle : 0.657 10.328 9235 Z= 0.339 Chirality : 0.044 0.157 1059 Planarity : 0.005 0.076 1175 Dihedral : 4.988 38.485 929 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.22 % Allowed : 32.28 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.03 (0.30), residues: 859 helix: -1.62 (0.70), residues: 38 sheet: 0.72 (0.26), residues: 416 loop : -0.62 (0.34), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 148 HIS 0.004 0.001 HIS B 198 PHE 0.019 0.002 PHE B 135 TYR 0.015 0.001 TYR B 140 ARG 0.004 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.9135 (t0) cc_final: 0.8861 (t0) REVERT: A 115 LYS cc_start: 0.8319 (mppt) cc_final: 0.7955 (mmtt) REVERT: B 148 TRP cc_start: 0.8175 (m100) cc_final: 0.7867 (m100) REVERT: H 72 ASP cc_start: 0.8211 (t0) cc_final: 0.7681 (t0) REVERT: H 75 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8478 (mtmm) REVERT: L 119 PRO cc_start: 0.8693 (Cg_endo) cc_final: 0.8460 (Cg_exo) REVERT: L 139 PHE cc_start: 0.8225 (p90) cc_final: 0.7998 (p90) outliers start: 32 outliers final: 18 residues processed: 186 average time/residue: 0.1866 time to fit residues: 45.4819 Evaluate side-chains 161 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 68 optimal weight: 0.3980 chunk 75 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6780 Z= 0.180 Angle : 0.625 7.555 9235 Z= 0.317 Chirality : 0.044 0.153 1059 Planarity : 0.005 0.059 1175 Dihedral : 4.754 37.876 927 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.53 % Allowed : 32.02 % Favored : 62.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.02 (0.30), residues: 859 helix: -1.61 (0.73), residues: 38 sheet: 0.79 (0.26), residues: 415 loop : -0.61 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 148 HIS 0.003 0.001 HIS A 35 PHE 0.013 0.001 PHE B 135 TYR 0.014 0.001 TYR B 140 ARG 0.005 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8307 (mppt) cc_final: 0.7963 (mmtt) REVERT: A 205 LYS cc_start: 0.9039 (mtmm) cc_final: 0.8772 (mtmm) REVERT: B 105 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: B 108 ARG cc_start: 0.7798 (ptm-80) cc_final: 0.7597 (ptm-80) REVERT: B 148 TRP cc_start: 0.8281 (m100) cc_final: 0.7775 (m100) REVERT: B 181 LEU cc_start: 0.9393 (mt) cc_final: 0.9150 (pt) REVERT: H 72 ASP cc_start: 0.8215 (t0) cc_final: 0.7738 (t0) REVERT: H 117 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7326 (pptt) REVERT: L 3 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: L 82 ASP cc_start: 0.7705 (m-30) cc_final: 0.7360 (m-30) REVERT: L 119 PRO cc_start: 0.8772 (Cg_endo) cc_final: 0.8524 (Cg_exo) REVERT: L 136 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8132 (pp) REVERT: L 139 PHE cc_start: 0.8293 (p90) cc_final: 0.7954 (p90) outliers start: 42 outliers final: 27 residues processed: 186 average time/residue: 0.1878 time to fit residues: 45.5299 Evaluate side-chains 173 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 6780 Z= 0.470 Angle : 0.710 6.917 9235 Z= 0.368 Chirality : 0.045 0.153 1059 Planarity : 0.005 0.052 1175 Dihedral : 5.139 40.569 927 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 7.91 % Allowed : 30.70 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.09 (0.30), residues: 859 helix: -1.70 (0.75), residues: 38 sheet: 0.69 (0.26), residues: 403 loop : -0.62 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.006 0.001 HIS B 198 PHE 0.015 0.002 PHE B 135 TYR 0.016 0.002 TYR B 87 ARG 0.003 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 155 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8790 (t0) cc_final: 0.8477 (t0) REVERT: A 115 LYS cc_start: 0.8434 (mppt) cc_final: 0.8056 (mmtt) REVERT: A 205 LYS cc_start: 0.9064 (mtmm) cc_final: 0.8774 (mtmm) REVERT: B 105 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: B 181 LEU cc_start: 0.9386 (mt) cc_final: 0.9147 (pt) REVERT: B 211 ARG cc_start: 0.5714 (mmm-85) cc_final: 0.5066 (mtp180) REVERT: H 38 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8451 (ptt90) REVERT: H 117 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7455 (pptt) REVERT: L 70 ASP cc_start: 0.8533 (m-30) cc_final: 0.8175 (p0) REVERT: L 105 GLU cc_start: 0.8445 (mp0) cc_final: 0.7959 (mp0) REVERT: L 119 PRO cc_start: 0.8901 (Cg_endo) cc_final: 0.8646 (Cg_exo) REVERT: L 139 PHE cc_start: 0.8444 (p90) cc_final: 0.8107 (p90) outliers start: 60 outliers final: 39 residues processed: 198 average time/residue: 0.2121 time to fit residues: 54.9169 Evaluate side-chains 184 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 142 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6780 Z= 0.308 Angle : 0.666 9.853 9235 Z= 0.341 Chirality : 0.044 0.149 1059 Planarity : 0.004 0.048 1175 Dihedral : 5.082 41.093 927 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 7.25 % Allowed : 30.70 % Favored : 62.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.30), residues: 859 helix: -1.70 (0.76), residues: 38 sheet: 0.77 (0.26), residues: 402 loop : -0.62 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.004 0.001 HIS B 198 PHE 0.012 0.002 PHE H 78 TYR 0.016 0.001 TYR B 140 ARG 0.004 0.000 ARG A 82B *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 147 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 86 ASP cc_start: 0.8754 (t0) cc_final: 0.8447 (t0) REVERT: A 95 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8729 (tt) REVERT: A 115 LYS cc_start: 0.8443 (mppt) cc_final: 0.8043 (mmtt) REVERT: A 205 LYS cc_start: 0.9051 (mtmm) cc_final: 0.8787 (mtmm) REVERT: B 105 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: B 108 ARG cc_start: 0.7902 (ptm-80) cc_final: 0.7683 (ptm-80) REVERT: B 170 ASP cc_start: 0.8870 (t0) cc_final: 0.8466 (t0) REVERT: B 181 LEU cc_start: 0.9459 (mt) cc_final: 0.9171 (pt) REVERT: B 211 ARG cc_start: 0.5604 (mmm-85) cc_final: 0.4948 (mtp180) REVERT: H 38 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8484 (ptt90) REVERT: H 117 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7437 (pptt) REVERT: L 3 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: L 47 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8654 (mp) REVERT: L 105 GLU cc_start: 0.8455 (mp0) cc_final: 0.7966 (mp0) REVERT: L 119 PRO cc_start: 0.8927 (Cg_endo) cc_final: 0.8666 (Cg_exo) outliers start: 55 outliers final: 38 residues processed: 188 average time/residue: 0.1891 time to fit residues: 46.9533 Evaluate side-chains 183 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 139 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 0.0270 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6780 Z= 0.203 Angle : 0.651 9.488 9235 Z= 0.328 Chirality : 0.044 0.150 1059 Planarity : 0.005 0.054 1175 Dihedral : 4.953 41.427 927 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 6.06 % Allowed : 31.62 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.03 (0.30), residues: 859 helix: -1.73 (0.77), residues: 38 sheet: 0.84 (0.26), residues: 405 loop : -0.60 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 148 HIS 0.003 0.001 HIS B 198 PHE 0.014 0.002 PHE B 135 TYR 0.016 0.001 TYR A 53 ARG 0.003 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 144 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 95 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8649 (tt) REVERT: A 115 LYS cc_start: 0.8418 (mppt) cc_final: 0.8031 (mmtt) REVERT: A 205 LYS cc_start: 0.9024 (mtmm) cc_final: 0.8775 (mtmm) REVERT: B 108 ARG cc_start: 0.7860 (ptm-80) cc_final: 0.7647 (ptm-80) REVERT: B 170 ASP cc_start: 0.8809 (t0) cc_final: 0.8595 (t0) REVERT: B 181 LEU cc_start: 0.9434 (mt) cc_final: 0.9142 (pt) REVERT: B 211 ARG cc_start: 0.5487 (mmm-85) cc_final: 0.4862 (mtp180) REVERT: H 38 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8486 (ptt90) REVERT: H 117 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7415 (pptt) REVERT: L 3 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: L 119 PRO cc_start: 0.8945 (Cg_endo) cc_final: 0.8672 (Cg_exo) outliers start: 46 outliers final: 31 residues processed: 178 average time/residue: 0.2061 time to fit residues: 47.3720 Evaluate side-chains 170 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.0010 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 0.0020 chunk 80 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6780 Z= 0.176 Angle : 0.647 9.731 9235 Z= 0.326 Chirality : 0.043 0.146 1059 Planarity : 0.004 0.045 1175 Dihedral : 4.785 39.097 927 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.93 % Allowed : 31.75 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.16 (0.30), residues: 859 helix: -1.74 (0.77), residues: 38 sheet: 0.93 (0.26), residues: 405 loop : -0.52 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 148 HIS 0.002 0.001 HIS A 35 PHE 0.012 0.001 PHE B 135 TYR 0.013 0.001 TYR B 140 ARG 0.004 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 153 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 95 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 115 LYS cc_start: 0.8405 (mppt) cc_final: 0.8060 (mmtt) REVERT: A 205 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8777 (mtmm) REVERT: B 108 ARG cc_start: 0.7857 (ptm-80) cc_final: 0.7570 (ptm-80) REVERT: B 170 ASP cc_start: 0.8816 (t0) cc_final: 0.8343 (t0) REVERT: B 181 LEU cc_start: 0.9428 (mt) cc_final: 0.9143 (pt) REVERT: B 211 ARG cc_start: 0.5401 (mmm-85) cc_final: 0.4813 (mtp180) REVERT: H 38 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8482 (ptt90) REVERT: H 72 ASP cc_start: 0.8262 (t0) cc_final: 0.7854 (t0) REVERT: H 117 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7344 (pptt) REVERT: H 179 LEU cc_start: 0.9220 (pt) cc_final: 0.8740 (pp) REVERT: L 3 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7805 (mt0) REVERT: L 82 ASP cc_start: 0.7390 (m-30) cc_final: 0.6597 (m-30) REVERT: L 119 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8696 (Cg_exo) outliers start: 45 outliers final: 30 residues processed: 185 average time/residue: 0.1967 time to fit residues: 47.5978 Evaluate side-chains 176 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6780 Z= 0.274 Angle : 0.674 9.523 9235 Z= 0.341 Chirality : 0.044 0.141 1059 Planarity : 0.005 0.044 1175 Dihedral : 4.921 39.264 927 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 6.19 % Allowed : 32.02 % Favored : 61.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.03 (0.30), residues: 859 helix: -1.66 (0.79), residues: 37 sheet: 0.81 (0.26), residues: 413 loop : -0.61 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 148 HIS 0.004 0.001 HIS B 198 PHE 0.016 0.002 PHE B 135 TYR 0.020 0.001 TYR A 53 ARG 0.004 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8455 (mppt) cc_final: 0.8101 (mmtt) REVERT: A 205 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8798 (mtmm) REVERT: B 6 GLN cc_start: 0.8884 (pt0) cc_final: 0.8412 (pt0) REVERT: B 108 ARG cc_start: 0.7967 (ptm-80) cc_final: 0.7637 (ptm-80) REVERT: B 170 ASP cc_start: 0.8865 (t0) cc_final: 0.8372 (t0) REVERT: B 181 LEU cc_start: 0.9413 (mt) cc_final: 0.9150 (pt) REVERT: B 211 ARG cc_start: 0.5494 (mmm-85) cc_final: 0.4872 (mtp180) REVERT: H 38 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8469 (ptt90) REVERT: H 117 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7371 (pptt) REVERT: L 35 TRP cc_start: 0.8416 (OUTLIER) cc_final: 0.7792 (m-90) REVERT: L 82 ASP cc_start: 0.7223 (m-30) cc_final: 0.6931 (m-30) REVERT: L 119 PRO cc_start: 0.9000 (Cg_endo) cc_final: 0.8720 (Cg_exo) REVERT: L 139 PHE cc_start: 0.8344 (p90) cc_final: 0.8130 (p90) outliers start: 47 outliers final: 34 residues processed: 176 average time/residue: 0.1978 time to fit residues: 46.0479 Evaluate side-chains 172 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6780 Z= 0.196 Angle : 0.684 9.661 9235 Z= 0.341 Chirality : 0.044 0.144 1059 Planarity : 0.005 0.044 1175 Dihedral : 4.856 38.696 927 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.01 % Allowed : 33.20 % Favored : 61.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.13 (0.30), residues: 859 helix: -1.70 (0.79), residues: 37 sheet: 0.93 (0.26), residues: 413 loop : -0.60 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 148 HIS 0.002 0.001 HIS B 198 PHE 0.023 0.002 PHE L 118 TYR 0.020 0.001 TYR A 53 ARG 0.004 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8417 (mppt) cc_final: 0.8069 (mmtt) REVERT: B 6 GLN cc_start: 0.8791 (pt0) cc_final: 0.8192 (pt0) REVERT: B 108 ARG cc_start: 0.7911 (ptm-80) cc_final: 0.7581 (ptm-80) REVERT: B 170 ASP cc_start: 0.8859 (t0) cc_final: 0.8324 (t0) REVERT: B 181 LEU cc_start: 0.9404 (mt) cc_final: 0.9143 (pt) REVERT: B 211 ARG cc_start: 0.5433 (mmm-85) cc_final: 0.4824 (mtp180) REVERT: H 38 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8459 (ptt90) REVERT: H 117 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7251 (pptt) REVERT: L 35 TRP cc_start: 0.8324 (OUTLIER) cc_final: 0.7804 (m-90) REVERT: L 119 PRO cc_start: 0.8983 (Cg_endo) cc_final: 0.8690 (Cg_exo) outliers start: 38 outliers final: 32 residues processed: 167 average time/residue: 0.1715 time to fit residues: 38.3844 Evaluate side-chains 169 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6780 Z= 0.312 Angle : 0.714 9.637 9235 Z= 0.359 Chirality : 0.045 0.144 1059 Planarity : 0.005 0.052 1175 Dihedral : 5.029 39.131 927 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.87 % Allowed : 33.60 % Favored : 61.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.08 (0.30), residues: 859 helix: -1.62 (0.81), residues: 37 sheet: 0.90 (0.26), residues: 414 loop : -0.67 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 148 HIS 0.004 0.001 HIS B 198 PHE 0.029 0.002 PHE L 118 TYR 0.020 0.002 TYR A 53 ARG 0.006 0.001 ARG B 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 142 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8799 (t0) cc_final: 0.8431 (t70) REVERT: A 115 LYS cc_start: 0.8439 (mppt) cc_final: 0.8126 (mmtt) REVERT: A 143 LYS cc_start: 0.7582 (mmmm) cc_final: 0.7270 (mmmt) REVERT: B 6 GLN cc_start: 0.8928 (pt0) cc_final: 0.8477 (pt0) REVERT: B 102 THR cc_start: 0.9358 (p) cc_final: 0.9100 (p) REVERT: B 108 ARG cc_start: 0.8033 (ptm-80) cc_final: 0.7764 (ptm-80) REVERT: B 149 LYS cc_start: 0.7258 (tttm) cc_final: 0.6795 (tptp) REVERT: B 170 ASP cc_start: 0.8854 (t0) cc_final: 0.8493 (t0) REVERT: B 181 LEU cc_start: 0.9404 (mt) cc_final: 0.9143 (pt) REVERT: B 211 ARG cc_start: 0.5626 (mmm-85) cc_final: 0.5110 (mtp85) REVERT: H 38 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8471 (ptt90) REVERT: H 117 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7354 (pptt) REVERT: H 155 TRP cc_start: 0.7728 (m-90) cc_final: 0.7060 (m-90) REVERT: H 179 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8786 (pp) REVERT: L 35 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.7855 (m-90) REVERT: L 82 ASP cc_start: 0.7463 (m-30) cc_final: 0.7183 (m-30) REVERT: L 116 PHE cc_start: 0.8161 (m-80) cc_final: 0.7751 (m-10) REVERT: L 166 GLN cc_start: 0.8736 (tt0) cc_final: 0.8520 (tt0) outliers start: 37 outliers final: 33 residues processed: 168 average time/residue: 0.1883 time to fit residues: 41.8891 Evaluate side-chains 177 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 180 SER Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109447 restraints weight = 9563.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.105560 restraints weight = 9450.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107206 restraints weight = 10607.844| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6780 Z= 0.212 Angle : 0.713 9.759 9235 Z= 0.353 Chirality : 0.045 0.180 1059 Planarity : 0.005 0.046 1175 Dihedral : 4.976 38.900 927 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.01 % Allowed : 33.73 % Favored : 61.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.13 (0.30), residues: 859 helix: -1.72 (0.83), residues: 35 sheet: 0.89 (0.26), residues: 413 loop : -0.55 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 148 HIS 0.003 0.001 HIS B 198 PHE 0.029 0.002 PHE L 139 TYR 0.018 0.001 TYR A 53 ARG 0.006 0.000 ARG B 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1766.19 seconds wall clock time: 32 minutes 30.68 seconds (1950.68 seconds total)