Starting phenix.real_space_refine on Fri Nov 15 01:15:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmi_45749/11_2024/9cmi_45749.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmi_45749/11_2024/9cmi_45749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmi_45749/11_2024/9cmi_45749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmi_45749/11_2024/9cmi_45749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmi_45749/11_2024/9cmi_45749.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cmi_45749/11_2024/9cmi_45749.cif" } resolution = 2.83 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= 0.009 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 32 5.16 5 C 4991 2.51 5 N 1302 2.21 5 O 1552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7877 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1324 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "B" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2244 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain: "H" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "K" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.41, per 1000 atoms: 0.69 Number of scatterers: 7877 At special positions: 0 Unit cell: (78.565, 139.763, 148.033, 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 32 16.00 O 1552 8.00 N 1302 7.00 C 4991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 64 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 113 " distance=2.03 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.09 Conformation dependent library (CDL) restraints added in 1.0 seconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 21 sheets defined 16.8% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.693A pdb=" N ALA A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 149 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 161 through 183 removed outlier: 3.891A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.560A pdb=" N ASN B 173 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 4.281A pdb=" N ASN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 137 Processing helix chain 'H' and resid 242 through 244 No H-bonds generated for 'chain 'H' and resid 242 through 244' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.841A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 153 Processing helix chain 'L' and resid 208 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 82 through 86 removed outlier: 5.192A pdb=" N ILE B 83 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER B 154 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 143 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP B 152 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 141 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B 154 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR B 139 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 41 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 63 removed outlier: 6.310A pdb=" N VAL B 57 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA B 134 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 78 Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 208 removed outlier: 7.147A pdb=" N ALA B 205 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS B 241 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLU B 207 " --> pdb=" O HIS B 241 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N THR B 243 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 297 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE B 261 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLN B 276 " --> pdb=" O PHE B 261 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 263 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 227 Processing sheet with id=AA9, first strand: chain 'H' and resid 29 through 33 removed outlier: 3.590A pdb=" N CYS H 48 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 84 through 86 removed outlier: 6.589A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 84 through 86 removed outlier: 6.589A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.784A pdb=" N SER H 220 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 190 through 194 removed outlier: 4.240A pdb=" N TYR H 234 " --> pdb=" O VAL H 251 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.637A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.951A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 11 removed outlier: 4.370A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 29 through 32 Processing sheet with id=AB9, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.797A pdb=" N LEU L 36 " --> pdb=" O GLU L 130 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP L 60 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.797A pdb=" N LEU L 36 " --> pdb=" O GLU L 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR L 122 " --> pdb=" O GLN L 115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 139 through 143 removed outlier: 5.105A pdb=" N SER L 156 " --> pdb=" O LEU L 206 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU L 206 " --> pdb=" O SER L 156 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL L 158 " --> pdb=" O LEU L 204 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU L 204 " --> pdb=" O VAL L 158 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU L 160 " --> pdb=" O SER L 202 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER L 202 " --> pdb=" O LEU L 160 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN L 162 " --> pdb=" O LEU L 200 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU L 200 " --> pdb=" O ASN L 162 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 169 through 175 363 hydrogen bonds defined for protein. 972 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: 2.22 Time building geometry restraints manager: 2.38 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: 2499 1.34 - 1.46: 1890 1.46 - 1.58: 3612 1.58 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 8046 Sorted by residual: bond pdb=" N ASN B 222 " pdb=" CA ASN B 222 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.20e-02 6.94e+03 8.11e+00 bond pdb=" N SER L 119 " pdb=" CA SER L 119 " ideal model delta sigma weight residual 1.458 1.485 -0.028 1.00e-02 1.00e+04 7.57e+00 bond pdb=" N ASN B 218 " pdb=" CA ASN B 218 " ideal model delta sigma weight residual 1.452 1.491 -0.039 1.41e-02 5.03e+03 7.47e+00 bond pdb=" N SER B 217 " pdb=" CA SER B 217 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.16e-02 7.43e+03 5.91e+00 bond pdb=" N SER L 117 " pdb=" CA SER L 117 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.70e+00 ... (remaining 8041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.38: 10934 6.38 - 12.77: 1 12.77 - 19.15: 0 19.15 - 25.53: 3 25.53 - 31.92: 3 Bond angle restraints: 10941 Sorted by residual: angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBS AV0 H 301 " ideal model delta sigma weight residual 110.52 78.60 31.92 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBR AV0 H 301 " ideal model delta sigma weight residual 107.79 80.57 27.22 3.00e+00 1.11e-01 8.23e+01 angle pdb=" CBR AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 110.70 84.18 26.52 3.00e+00 1.11e-01 7.81e+01 angle pdb=" CBS AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 105.72 80.46 25.26 3.00e+00 1.11e-01 7.09e+01 angle pdb=" CBR AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBS AV0 H 301 " ideal model delta sigma weight residual 110.98 133.27 -22.29 3.00e+00 1.11e-01 5.52e+01 ... (remaining 10936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.25: 4525 22.25 - 44.50: 246 44.50 - 66.75: 34 66.75 - 89.00: 18 89.00 - 111.25: 9 Dihedral angle restraints: 4832 sinusoidal: 1886 harmonic: 2946 Sorted by residual: dihedral pdb=" OAS AV0 H 301 " pdb=" CCT AV0 H 301 " pdb=" CCV AV0 H 301 " pdb=" OAU AV0 H 301 " ideal model delta sinusoidal sigma weight residual 59.49 170.74 -111.25 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" CCN AV0 H 301 " pdb=" CCT AV0 H 301 " pdb=" CCV AV0 H 301 " pdb=" OAU AV0 H 301 " ideal model delta sinusoidal sigma weight residual 178.46 -70.35 -111.19 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" CCR AV0 H 301 " pdb=" CCT AV0 H 301 " pdb=" CCV AV0 H 301 " pdb=" OAS AV0 H 301 " ideal model delta sinusoidal sigma weight residual 174.22 63.24 110.98 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 4829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 727 0.030 - 0.059: 343 0.059 - 0.089: 110 0.089 - 0.118: 65 0.118 - 0.148: 9 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA VAL A 56 " pdb=" N VAL A 56 " pdb=" C VAL A 56 " pdb=" CB VAL A 56 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE L 46 " pdb=" N ILE L 46 " pdb=" C ILE L 46 " pdb=" CB ILE L 46 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1251 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 188 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO H 189 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 189 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 189 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 272 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C VAL B 272 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 272 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS B 273 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 68 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO L 69 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 69 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 69 " 0.021 5.00e-02 4.00e+02 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 499 2.73 - 3.27: 7674 3.27 - 3.82: 13236 3.82 - 4.36: 16040 4.36 - 4.90: 28038 Nonbonded interactions: 65487 Sorted by model distance: nonbonded pdb=" OD2 ASP H 141 " pdb=" OH TYR L 61 " model vdw 2.188 3.040 nonbonded pdb=" OD1 ASP B 292 " pdb=" OH TYR B 296 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR B 156 " pdb=" OE2 GLU B 184 " model vdw 2.229 3.040 nonbonded pdb=" OG SER L 39 " pdb=" OD2 ASP L 42 " model vdw 2.247 3.040 nonbonded pdb=" NH1 ARG B 143 " pdb=" OD2 ASP B 151 " model vdw 2.251 3.120 ... (remaining 65482 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.760 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.003 0.042 8046 Z= 0.217 Angle : 0.822 31.916 10941 Z= 0.383 Chirality : 0.042 0.148 1254 Planarity : 0.004 0.043 1373 Dihedral : 15.697 111.252 2936 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 1.04 % Allowed : 9.15 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.87 (0.26), residues: 1015 helix: 1.94 (0.42), residues: 156 sheet: -0.67 (0.25), residues: 409 loop : -1.32 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 125 HIS 0.004 0.001 HIS H 61 PHE 0.014 0.001 PHE B 316 TYR 0.010 0.001 TYR L 111 ARG 0.002 0.000 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8443 (ptp) cc_final: 0.8214 (mtp) REVERT: A 146 ASP cc_start: 0.7780 (t70) cc_final: 0.7574 (t0) REVERT: B 97 GLN cc_start: 0.8816 (tt0) cc_final: 0.8576 (tt0) REVERT: B 110 GLU cc_start: 0.8485 (tp30) cc_final: 0.8268 (tm-30) REVERT: B 234 TRP cc_start: 0.8432 (p-90) cc_final: 0.8014 (p-90) REVERT: H 54 ASN cc_start: 0.7471 (t0) cc_final: 0.7100 (p0) REVERT: H 102 LYS cc_start: 0.9181 (mmpt) cc_final: 0.8908 (mmpt) REVERT: H 115 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8495 (mp0) REVERT: H 241 LYS cc_start: 0.8086 (tptp) cc_final: 0.7823 (tppt) REVERT: K 31 ARG cc_start: 0.8378 (mmp-170) cc_final: 0.8064 (mmp80) REVERT: K 95 TYR cc_start: 0.7842 (m-80) cc_final: 0.7274 (m-80) REVERT: L 192 ASP cc_start: 0.7732 (t0) cc_final: 0.7448 (t0) outliers start: 9 outliers final: 3 residues processed: 143 average time/residue: 1.1045 time to fit residues: 168.2773 Evaluate side-chains 98 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain H residue 190 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 GLN L 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8046 Z= 0.192 Angle : 0.833 31.655 10941 Z= 0.356 Chirality : 0.042 0.168 1254 Planarity : 0.004 0.042 1373 Dihedral : 8.201 93.065 1231 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.01 % Allowed : 15.41 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.69 (0.26), residues: 1015 helix: 2.09 (0.43), residues: 155 sheet: -0.55 (0.25), residues: 414 loop : -1.21 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 125 HIS 0.006 0.001 HIS H 61 PHE 0.014 0.001 PHE K 37 TYR 0.012 0.001 TYR B 133 ARG 0.008 0.001 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 GLN cc_start: 0.8809 (tt0) cc_final: 0.8559 (tt0) REVERT: B 126 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: B 234 TRP cc_start: 0.8460 (p-90) cc_final: 0.8052 (p-90) REVERT: H 54 ASN cc_start: 0.7402 (t0) cc_final: 0.7089 (p0) REVERT: H 102 LYS cc_start: 0.9159 (mmpt) cc_final: 0.8828 (mmmt) REVERT: H 115 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8452 (mp0) REVERT: H 241 LYS cc_start: 0.8081 (tptp) cc_final: 0.7786 (tppt) REVERT: K 19 ARG cc_start: 0.8185 (mmt90) cc_final: 0.7983 (mmt90) REVERT: K 31 ARG cc_start: 0.8224 (mmp-170) cc_final: 0.7920 (mmp80) REVERT: K 34 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7700 (mtp) REVERT: K 83 MET cc_start: 0.9288 (mtp) cc_final: 0.9025 (mtp) REVERT: K 95 TYR cc_start: 0.7849 (m-80) cc_final: 0.7305 (m-80) REVERT: L 168 GLU cc_start: 0.8129 (mp0) cc_final: 0.6991 (pp20) outliers start: 26 outliers final: 9 residues processed: 117 average time/residue: 1.1262 time to fit residues: 140.8344 Evaluate side-chains 98 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 HIS ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8046 Z= 0.189 Angle : 0.813 31.562 10941 Z= 0.346 Chirality : 0.042 0.173 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.540 95.892 1229 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.13 % Allowed : 17.27 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.53 (0.26), residues: 1015 helix: 2.11 (0.42), residues: 155 sheet: -0.42 (0.26), residues: 416 loop : -1.11 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 125 HIS 0.003 0.001 HIS H 61 PHE 0.013 0.001 PHE B 316 TYR 0.010 0.001 TYR B 133 ARG 0.009 0.000 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6764 (OUTLIER) cc_final: 0.6483 (p) REVERT: B 126 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: B 234 TRP cc_start: 0.8482 (p-90) cc_final: 0.8082 (p-90) REVERT: B 263 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7960 (mp) REVERT: B 284 ASP cc_start: 0.8936 (m-30) cc_final: 0.8723 (m-30) REVERT: H 54 ASN cc_start: 0.7464 (t0) cc_final: 0.7133 (p0) REVERT: H 102 LYS cc_start: 0.9142 (mmpt) cc_final: 0.8803 (mmmt) REVERT: H 115 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8485 (mp0) REVERT: H 241 LYS cc_start: 0.8094 (tptp) cc_final: 0.7799 (tppt) REVERT: H 252 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7867 (tm-30) REVERT: K 19 ARG cc_start: 0.8213 (mmt90) cc_final: 0.7887 (mmt90) REVERT: K 31 ARG cc_start: 0.8246 (mmp-170) cc_final: 0.7940 (mmp80) REVERT: K 34 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8001 (mtp) REVERT: K 83 MET cc_start: 0.9305 (mtp) cc_final: 0.9095 (mtp) REVERT: K 95 TYR cc_start: 0.7852 (m-80) cc_final: 0.7287 (m-80) REVERT: L 29 MET cc_start: 0.7422 (mmm) cc_final: 0.6835 (mpp) REVERT: L 168 GLU cc_start: 0.8173 (mp0) cc_final: 0.7098 (pp20) outliers start: 27 outliers final: 10 residues processed: 111 average time/residue: 1.0973 time to fit residues: 130.1849 Evaluate side-chains 100 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8046 Z= 0.193 Angle : 0.829 31.573 10941 Z= 0.349 Chirality : 0.042 0.178 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.628 95.249 1229 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.01 % Allowed : 19.12 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.46 (0.27), residues: 1015 helix: 2.11 (0.42), residues: 155 sheet: -0.32 (0.26), residues: 417 loop : -1.09 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 PHE 0.013 0.001 PHE B 316 TYR 0.015 0.001 TYR H 59 ARG 0.009 0.000 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6814 (OUTLIER) cc_final: 0.6540 (p) REVERT: B 126 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: B 234 TRP cc_start: 0.8488 (p-90) cc_final: 0.8095 (p-90) REVERT: B 263 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7941 (mp) REVERT: B 284 ASP cc_start: 0.8906 (m-30) cc_final: 0.8705 (m-30) REVERT: H 54 ASN cc_start: 0.7428 (t0) cc_final: 0.6857 (p0) REVERT: H 57 SER cc_start: 0.9119 (t) cc_final: 0.8559 (m) REVERT: H 69 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7670 (ptmm) REVERT: H 102 LYS cc_start: 0.9115 (mmpt) cc_final: 0.8791 (mmmt) REVERT: H 115 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8551 (mp0) REVERT: H 241 LYS cc_start: 0.8083 (tptp) cc_final: 0.7788 (tppt) REVERT: K 19 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7877 (mmt90) REVERT: K 31 ARG cc_start: 0.8247 (mmp-170) cc_final: 0.7943 (mmp80) REVERT: K 34 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7993 (mtp) REVERT: K 95 TYR cc_start: 0.7839 (m-80) cc_final: 0.7291 (m-80) REVERT: L 29 MET cc_start: 0.7358 (mmm) cc_final: 0.7103 (mtp) REVERT: L 42 ASP cc_start: 0.8143 (t0) cc_final: 0.7794 (t0) REVERT: L 168 GLU cc_start: 0.8185 (mp0) cc_final: 0.7104 (pp20) outliers start: 26 outliers final: 13 residues processed: 108 average time/residue: 0.9897 time to fit residues: 115.2253 Evaluate side-chains 105 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.0470 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 78 GLN K 39 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8046 Z= 0.218 Angle : 0.832 31.665 10941 Z= 0.352 Chirality : 0.042 0.179 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.634 95.533 1229 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.01 % Allowed : 19.93 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.41 (0.27), residues: 1015 helix: 1.99 (0.42), residues: 155 sheet: -0.24 (0.27), residues: 411 loop : -1.06 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 125 HIS 0.004 0.001 HIS B 285 PHE 0.014 0.001 PHE B 316 TYR 0.009 0.001 TYR B 133 ARG 0.010 0.000 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6881 (OUTLIER) cc_final: 0.6621 (p) REVERT: B 126 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: B 234 TRP cc_start: 0.8499 (p-90) cc_final: 0.8119 (p-90) REVERT: B 263 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7885 (mp) REVERT: H 54 ASN cc_start: 0.7436 (t0) cc_final: 0.6891 (p0) REVERT: H 57 SER cc_start: 0.9019 (t) cc_final: 0.8496 (m) REVERT: H 86 TYR cc_start: 0.9074 (m-80) cc_final: 0.8845 (m-80) REVERT: H 102 LYS cc_start: 0.9115 (mmpt) cc_final: 0.8798 (mmmt) REVERT: H 115 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8560 (mp0) REVERT: H 241 LYS cc_start: 0.8089 (tptp) cc_final: 0.7786 (tppt) REVERT: K 19 ARG cc_start: 0.8093 (mmt90) cc_final: 0.7881 (mmt90) REVERT: K 31 ARG cc_start: 0.8270 (mmp-170) cc_final: 0.8025 (mmm-85) REVERT: K 34 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7397 (mtp) REVERT: K 95 TYR cc_start: 0.7827 (m-80) cc_final: 0.7261 (m-80) REVERT: K 110 TYR cc_start: 0.8807 (m-80) cc_final: 0.8594 (m-80) REVERT: L 42 ASP cc_start: 0.8183 (t0) cc_final: 0.7818 (t0) REVERT: L 114 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6570 (pt0) REVERT: L 168 GLU cc_start: 0.8184 (mp0) cc_final: 0.7150 (pp20) outliers start: 26 outliers final: 14 residues processed: 109 average time/residue: 1.0620 time to fit residues: 123.9896 Evaluate side-chains 104 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.0000 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8046 Z= 0.180 Angle : 0.823 31.527 10941 Z= 0.347 Chirality : 0.041 0.180 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.621 95.553 1229 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.13 % Allowed : 20.74 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.35 (0.27), residues: 1015 helix: 2.06 (0.42), residues: 155 sheet: -0.10 (0.27), residues: 406 loop : -1.13 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 PHE 0.013 0.001 PHE B 316 TYR 0.011 0.001 TYR K 32 ARG 0.009 0.000 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6495 (p) REVERT: A 126 LEU cc_start: 0.7196 (mt) cc_final: 0.6878 (mp) REVERT: B 126 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: B 234 TRP cc_start: 0.8464 (p-90) cc_final: 0.8094 (p-90) REVERT: B 244 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7583 (mm) REVERT: H 54 ASN cc_start: 0.7422 (t0) cc_final: 0.6894 (p0) REVERT: H 57 SER cc_start: 0.8868 (t) cc_final: 0.8350 (m) REVERT: H 69 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7677 (ptmm) REVERT: H 86 TYR cc_start: 0.9038 (m-80) cc_final: 0.8817 (m-80) REVERT: H 102 LYS cc_start: 0.9135 (mmpt) cc_final: 0.8817 (mmmt) REVERT: H 115 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8548 (mp0) REVERT: H 232 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7839 (tp-100) REVERT: H 241 LYS cc_start: 0.8091 (tptp) cc_final: 0.7800 (tppt) REVERT: K 19 ARG cc_start: 0.8079 (mmt90) cc_final: 0.7860 (mmt90) REVERT: K 31 ARG cc_start: 0.8257 (mmp-170) cc_final: 0.8012 (mmm-85) REVERT: K 34 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7305 (mtp) REVERT: K 95 TYR cc_start: 0.7827 (m-80) cc_final: 0.7258 (m-80) REVERT: L 42 ASP cc_start: 0.8206 (t0) cc_final: 0.7852 (t0) REVERT: L 114 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6537 (pt0) REVERT: L 168 GLU cc_start: 0.8202 (mp0) cc_final: 0.7168 (pp20) outliers start: 27 outliers final: 13 residues processed: 114 average time/residue: 0.9560 time to fit residues: 117.4339 Evaluate side-chains 106 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 0.0570 chunk 58 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8046 Z= 0.163 Angle : 0.819 31.463 10941 Z= 0.345 Chirality : 0.041 0.182 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.617 94.822 1229 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.67 % Allowed : 21.67 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.19 (0.27), residues: 1015 helix: 2.14 (0.42), residues: 155 sheet: 0.06 (0.27), residues: 403 loop : -1.07 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 PHE 0.013 0.001 PHE B 316 TYR 0.010 0.001 TYR B 133 ARG 0.011 0.000 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 THR cc_start: 0.6760 (OUTLIER) cc_final: 0.6476 (p) REVERT: A 126 LEU cc_start: 0.7252 (mt) cc_final: 0.6943 (mp) REVERT: B 126 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: B 234 TRP cc_start: 0.8464 (p-90) cc_final: 0.8099 (p-90) REVERT: H 54 ASN cc_start: 0.7411 (t0) cc_final: 0.6875 (p0) REVERT: H 57 SER cc_start: 0.8720 (t) cc_final: 0.8288 (m) REVERT: H 102 LYS cc_start: 0.9114 (mmpt) cc_final: 0.8881 (mmpt) REVERT: H 115 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8561 (mp0) REVERT: H 232 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7862 (tp-100) REVERT: H 241 LYS cc_start: 0.8097 (tptp) cc_final: 0.7806 (tppt) REVERT: K 31 ARG cc_start: 0.8222 (mmp-170) cc_final: 0.8007 (mmm-85) REVERT: K 34 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7791 (mtp) REVERT: K 83 MET cc_start: 0.9168 (mtp) cc_final: 0.8730 (mtp) REVERT: K 95 TYR cc_start: 0.7829 (m-80) cc_final: 0.7241 (m-80) REVERT: L 42 ASP cc_start: 0.8212 (t0) cc_final: 0.7859 (t0) REVERT: L 114 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6445 (pt0) REVERT: L 168 GLU cc_start: 0.8204 (mp0) cc_final: 0.7176 (pp20) REVERT: L 180 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8092 (mp-120) outliers start: 23 outliers final: 14 residues processed: 110 average time/residue: 1.0497 time to fit residues: 124.1749 Evaluate side-chains 102 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 236 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 75 optimal weight: 0.0070 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN K 82 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8046 Z= 0.153 Angle : 0.817 31.402 10941 Z= 0.345 Chirality : 0.041 0.184 1254 Planarity : 0.004 0.041 1373 Dihedral : 7.317 97.138 1229 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.67 % Allowed : 21.90 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.07 (0.27), residues: 1015 helix: 2.24 (0.42), residues: 155 sheet: 0.19 (0.28), residues: 398 loop : -1.03 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 132 HIS 0.003 0.001 HIS B 285 PHE 0.012 0.001 PHE B 316 TYR 0.009 0.001 TYR L 198 ARG 0.010 0.000 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7471 (tpp) cc_final: 0.7215 (ttt) REVERT: A 105 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6510 (p) REVERT: A 126 LEU cc_start: 0.7282 (mt) cc_final: 0.6810 (mp) REVERT: B 126 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: B 234 TRP cc_start: 0.8443 (p-90) cc_final: 0.8088 (p-90) REVERT: H 54 ASN cc_start: 0.7389 (t0) cc_final: 0.6856 (p0) REVERT: H 57 SER cc_start: 0.8562 (t) cc_final: 0.8002 (m) REVERT: H 69 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7835 (mtmm) REVERT: H 102 LYS cc_start: 0.9124 (mmpt) cc_final: 0.8741 (mmmt) REVERT: H 115 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8543 (mp0) REVERT: H 241 LYS cc_start: 0.8077 (tptp) cc_final: 0.7787 (tppt) REVERT: K 19 ARG cc_start: 0.8226 (mmt90) cc_final: 0.8013 (tpp-160) REVERT: K 34 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7146 (ttm) REVERT: K 83 MET cc_start: 0.9171 (mtp) cc_final: 0.8772 (mtp) REVERT: K 95 TYR cc_start: 0.7849 (m-80) cc_final: 0.7263 (m-80) REVERT: L 42 ASP cc_start: 0.8220 (t0) cc_final: 0.7831 (t0) REVERT: L 114 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6424 (pt0) REVERT: L 168 GLU cc_start: 0.8223 (mp0) cc_final: 0.7091 (pp20) REVERT: L 180 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8502 (mp10) REVERT: L 192 ASP cc_start: 0.7728 (t0) cc_final: 0.7465 (t0) outliers start: 23 outliers final: 11 residues processed: 109 average time/residue: 1.0349 time to fit residues: 121.0035 Evaluate side-chains 103 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.0370 chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8046 Z= 0.205 Angle : 0.844 31.369 10941 Z= 0.362 Chirality : 0.042 0.179 1254 Planarity : 0.004 0.042 1373 Dihedral : 7.197 97.891 1229 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.09 % Allowed : 22.94 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.09 (0.27), residues: 1015 helix: 2.22 (0.42), residues: 155 sheet: 0.18 (0.28), residues: 398 loop : -1.06 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 PHE 0.014 0.001 PHE B 316 TYR 0.010 0.001 TYR H 59 ARG 0.010 0.001 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7517 (tpp) cc_final: 0.7236 (ttt) REVERT: A 105 THR cc_start: 0.6863 (OUTLIER) cc_final: 0.6568 (p) REVERT: A 126 LEU cc_start: 0.7277 (mt) cc_final: 0.6941 (mp) REVERT: B 126 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: B 234 TRP cc_start: 0.8474 (p-90) cc_final: 0.8118 (p-90) REVERT: H 54 ASN cc_start: 0.7353 (t0) cc_final: 0.6827 (p0) REVERT: H 57 SER cc_start: 0.8658 (t) cc_final: 0.8071 (m) REVERT: H 69 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7870 (mtmm) REVERT: H 102 LYS cc_start: 0.9139 (mmpt) cc_final: 0.8752 (mmmt) REVERT: H 115 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8584 (mp0) REVERT: H 241 LYS cc_start: 0.8077 (tptp) cc_final: 0.7780 (tppt) REVERT: K 34 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7746 (mtp) REVERT: K 83 MET cc_start: 0.9173 (mtp) cc_final: 0.8765 (mtp) REVERT: K 95 TYR cc_start: 0.7840 (m-80) cc_final: 0.7253 (m-80) REVERT: L 42 ASP cc_start: 0.8216 (t0) cc_final: 0.7877 (t0) REVERT: L 114 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6543 (pt0) REVERT: L 168 GLU cc_start: 0.8209 (mp0) cc_final: 0.7093 (pp20) REVERT: L 180 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8494 (mp10) REVERT: L 192 ASP cc_start: 0.7742 (t0) cc_final: 0.7477 (t0) outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 1.0675 time to fit residues: 116.7214 Evaluate side-chains 101 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 99 optimal weight: 0.1980 chunk 91 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN K 82 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8046 Z= 0.164 Angle : 0.842 31.279 10941 Z= 0.359 Chirality : 0.041 0.185 1254 Planarity : 0.004 0.041 1373 Dihedral : 6.957 97.170 1229 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.09 % Allowed : 22.83 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.01 (0.27), residues: 1015 helix: 2.30 (0.43), residues: 155 sheet: 0.24 (0.28), residues: 399 loop : -1.02 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 125 HIS 0.003 0.001 HIS B 285 PHE 0.012 0.001 PHE B 316 TYR 0.011 0.001 TYR H 59 ARG 0.011 0.001 ARG K 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7487 (tpp) cc_final: 0.7193 (ttt) REVERT: A 105 THR cc_start: 0.6801 (OUTLIER) cc_final: 0.6501 (p) REVERT: A 126 LEU cc_start: 0.7251 (mt) cc_final: 0.6757 (mp) REVERT: B 126 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: B 234 TRP cc_start: 0.8429 (p-90) cc_final: 0.8061 (p-90) REVERT: H 54 ASN cc_start: 0.7333 (t0) cc_final: 0.6791 (p0) REVERT: H 57 SER cc_start: 0.8463 (t) cc_final: 0.7879 (m) REVERT: H 102 LYS cc_start: 0.9145 (mmpt) cc_final: 0.8789 (mmmt) REVERT: H 115 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8576 (mp0) REVERT: H 169 LYS cc_start: 0.7448 (pptt) cc_final: 0.7221 (pmtt) REVERT: H 241 LYS cc_start: 0.8076 (tptp) cc_final: 0.7787 (tppt) REVERT: K 34 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7135 (ttm) REVERT: K 83 MET cc_start: 0.9189 (mtp) cc_final: 0.8845 (mtp) REVERT: K 95 TYR cc_start: 0.7838 (m-80) cc_final: 0.7238 (m-80) REVERT: L 42 ASP cc_start: 0.8217 (t0) cc_final: 0.7869 (t0) REVERT: L 114 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6442 (pt0) REVERT: L 168 GLU cc_start: 0.8215 (mp0) cc_final: 0.7071 (pp20) REVERT: L 180 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8307 (mm110) REVERT: L 192 ASP cc_start: 0.7752 (t0) cc_final: 0.7499 (t0) outliers start: 18 outliers final: 10 residues processed: 102 average time/residue: 1.1036 time to fit residues: 120.4170 Evaluate side-chains 101 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 114 GLN Chi-restraints excluded: chain L residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 81 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 69 optimal weight: 0.0060 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.122137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.089931 restraints weight = 15958.944| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.55 r_work: 0.3522 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8046 Z= 0.152 Angle : 0.839 31.154 10941 Z= 0.357 Chirality : 0.041 0.180 1254 Planarity : 0.004 0.041 1373 Dihedral : 6.802 95.374 1229 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.97 % Allowed : 22.71 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.08 (0.27), residues: 1015 helix: 2.32 (0.43), residues: 156 sheet: 0.29 (0.28), residues: 404 loop : -0.95 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 132 HIS 0.003 0.001 HIS H 127 PHE 0.012 0.001 PHE B 316 TYR 0.020 0.001 TYR H 59 ARG 0.010 0.001 ARG K 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.69 seconds wall clock time: 63 minutes 6.28 seconds (3786.28 seconds total)