Starting phenix.real_space_refine on Fri Dec 27 11:42:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0t_26950/12_2024/7v0t_26950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0t_26950/12_2024/7v0t_26950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v0t_26950/12_2024/7v0t_26950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0t_26950/12_2024/7v0t_26950.map" model { file = "/net/cci-nas-00/data/ceres_data/7v0t_26950/12_2024/7v0t_26950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0t_26950/12_2024/7v0t_26950.cif" } resolution = 2.7 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= 0.001 sd= 0.277 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 12 5.16 5 C 2941 2.51 5 N 805 2.21 5 O 900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4658 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2276 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2343 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Time building chain proxies: 3.87, per 1000 atoms: 0.83 Number of scatterers: 4658 At special positions: 0 Unit cell: (89.225, 82.585, 75.53, 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 12 16.00 O 900 8.00 N 805 7.00 C 2941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.22 Conformation dependent library (CDL) restraints added in 515.6 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 41.3% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.817A pdb=" N LYS E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 194 through 201 Processing helix chain 'E' and resid 277 through 291 Processing helix chain 'E' and resid 291 through 300 Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.738A pdb=" N LEU E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 335 through 349 removed outlier: 4.147A pdb=" N SER E 349 " --> pdb=" O ARG E 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.842A pdb=" N LYS C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.588A pdb=" N LEU C 167 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 201 Processing helix chain 'C' and resid 277 through 291 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.696A pdb=" N LEU C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.139A pdb=" N VAL C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 59 through 67 removed outlier: 6.493A pdb=" N VAL E 59 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG E 80 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU E 61 " --> pdb=" O ALA E 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 87 current: chain 'E' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 184 through 185 current: chain 'E' and resid 262 through 270 Processing sheet with id=AA2, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 66 removed outlier: 6.556A pdb=" N VAL C 59 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 61 " --> pdb=" O ALA C 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 87 current: chain 'C' and resid 224 through 234 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 224 through 234 current: chain 'C' and resid 262 through 270 164 hydrogen bonds defined for protein. 468 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: 1.21 Time building geometry restraints manager: 1.33 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: 1574 1.34 - 1.46: 884 1.46 - 1.58: 2235 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4713 Sorted by residual: bond pdb=" N PRO C 221 " pdb=" CA PRO C 221 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.31e-02 5.83e+03 1.61e+00 bond pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CG1 ILE C 140 " pdb=" CD1 ILE C 140 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" CA ILE C 216 " pdb=" CB ILE C 216 " ideal model delta sigma weight residual 1.540 1.568 -0.028 2.70e-02 1.37e+03 1.08e+00 bond pdb=" CG GLN E 124 " pdb=" CD GLN E 124 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 ... (remaining 4708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 6198 1.43 - 2.87: 160 2.87 - 4.30: 33 4.30 - 5.74: 9 5.74 - 7.17: 5 Bond angle restraints: 6405 Sorted by residual: angle pdb=" N ASN C 91 " pdb=" CA ASN C 91 " pdb=" C ASN C 91 " ideal model delta sigma weight residual 114.09 109.26 4.83 1.55e+00 4.16e-01 9.69e+00 angle pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " pdb=" CD GLN E 124 " ideal model delta sigma weight residual 112.60 117.66 -5.06 1.70e+00 3.46e-01 8.86e+00 angle pdb=" C LEU C 335 " pdb=" N VAL C 336 " pdb=" CA VAL C 336 " ideal model delta sigma weight residual 120.33 122.60 -2.27 8.00e-01 1.56e+00 8.06e+00 angle pdb=" CA GLN E 124 " pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " ideal model delta sigma weight residual 114.10 119.52 -5.42 2.00e+00 2.50e-01 7.34e+00 angle pdb=" CA PRO C 271 " pdb=" C PRO C 271 " pdb=" N GLU C 272 " ideal model delta sigma weight residual 114.74 117.11 -2.37 1.03e+00 9.43e-01 5.30e+00 ... (remaining 6400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2432 17.95 - 35.90: 294 35.90 - 53.86: 99 53.86 - 71.81: 29 71.81 - 89.76: 17 Dihedral angle restraints: 2871 sinusoidal: 1175 harmonic: 1696 Sorted by residual: dihedral pdb=" CA TRP E 81 " pdb=" C TRP E 81 " pdb=" N VAL E 82 " pdb=" CA VAL E 82 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CG ARG C 246 " pdb=" CD ARG C 246 " pdb=" NE ARG C 246 " pdb=" CZ ARG C 246 " ideal model delta sinusoidal sigma weight residual -90.00 -134.83 44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU C 32 " pdb=" CG GLU C 32 " pdb=" CD GLU C 32 " pdb=" OE1 GLU C 32 " ideal model delta sinusoidal sigma weight residual 0.00 88.72 -88.72 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 2868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 567 0.045 - 0.090: 123 0.090 - 0.135: 38 0.135 - 0.180: 4 0.180 - 0.225: 1 Chirality restraints: 733 Sorted by residual: chirality pdb=" CB ILE C 216 " pdb=" CA ILE C 216 " pdb=" CG1 ILE C 216 " pdb=" CG2 ILE C 216 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE E 276 " pdb=" CA ILE E 276 " pdb=" CG1 ILE E 276 " pdb=" CG2 ILE E 276 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 730 not shown) Planarity restraints: 840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 273 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO E 274 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 274 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 274 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 326 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO C 327 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 327 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 327 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 146 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 147 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 147 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 147 " -0.018 5.00e-02 4.00e+02 ... (remaining 837 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 138 2.70 - 3.25: 4322 3.25 - 3.80: 7907 3.80 - 4.35: 10331 4.35 - 4.90: 16454 Nonbonded interactions: 39152 Sorted by model distance: nonbonded pdb=" OG1 THR E 179 " pdb=" O ASP E 183 " model vdw 2.151 3.040 nonbonded pdb=" NE2 HIS E 275 " pdb=" OE1 GLU C 312 " model vdw 2.195 3.120 nonbonded pdb=" NH1 ARG C 233 " pdb=" O HOH C1001 " model vdw 2.271 3.120 nonbonded pdb=" O TYR C 46 " pdb=" O HOH C1002 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLU C 225 " pdb=" OH TYR C 299 " model vdw 2.293 3.040 ... (remaining 39147 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 56 through 203 or resid 217 through 348)) selection = (chain 'E' and ((resid 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 181 or resid 192 through 348)) } 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: 1.250 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.790 Find NCS groups from input model: 0.220 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:15.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.004 0.042 4713 Z= 0.246 Angle : 0.631 7.174 6405 Z= 0.333 Chirality : 0.042 0.225 733 Planarity : 0.005 0.036 840 Dihedral : 19.430 89.760 1763 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.57 % Favored : 98.26 % Rotamer: Outliers : 3.45 % Allowed : 27.79 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.33), residues: 574 helix: 0.62 (0.34), residues: 219 sheet: 1.76 (0.57), residues: 84 loop : -0.18 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.003 0.001 HIS E 163 PHE 0.022 0.002 PHE C 314 TYR 0.019 0.002 TYR E 278 ARG 0.004 0.001 ARG E 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.540 Fit side-chains REVERT: C 83 GLN cc_start: 0.7179 (mt0) cc_final: 0.6971 (mp10) REVERT: C 109 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8112 (mp0) outliers start: 17 outliers final: 12 residues processed: 84 average time/residue: 1.4190 time to fit residues: 123.4708 Evaluate side-chains 82 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 265 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.0010 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN E 275 HIS C 124 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4713 Z= 0.171 Angle : 0.517 6.553 6405 Z= 0.257 Chirality : 0.039 0.153 733 Planarity : 0.004 0.030 840 Dihedral : 6.947 55.006 648 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.06 % Allowed : 25.96 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.34), residues: 574 helix: 1.12 (0.35), residues: 220 sheet: 1.89 (0.58), residues: 84 loop : -0.04 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 81 HIS 0.002 0.001 HIS E 309 PHE 0.018 0.002 PHE C 314 TYR 0.012 0.001 TYR E 278 ARG 0.003 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.720 Fit side-chains REVERT: C 114 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8038 (m-80) outliers start: 20 outliers final: 11 residues processed: 84 average time/residue: 1.6744 time to fit residues: 145.2002 Evaluate side-chains 81 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 124 GLN C 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4713 Z= 0.132 Angle : 0.462 6.325 6405 Z= 0.229 Chirality : 0.037 0.148 733 Planarity : 0.003 0.029 840 Dihedral : 6.197 55.654 639 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.48 % Allowed : 25.35 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.35), residues: 574 helix: 1.42 (0.36), residues: 221 sheet: 1.58 (0.56), residues: 88 loop : 0.04 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 81 HIS 0.001 0.000 HIS E 309 PHE 0.017 0.002 PHE C 314 TYR 0.010 0.001 TYR E 278 ARG 0.003 0.000 ARG E 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.492 Fit side-chains REVERT: C 114 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: C 233 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7982 (mtt90) REVERT: C 300 MET cc_start: 0.8108 (mtt) cc_final: 0.7907 (mtp) outliers start: 27 outliers final: 13 residues processed: 90 average time/residue: 1.6782 time to fit residues: 156.2316 Evaluate side-chains 86 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 198 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4713 Z= 0.158 Angle : 0.491 6.713 6405 Z= 0.240 Chirality : 0.038 0.152 733 Planarity : 0.003 0.029 840 Dihedral : 6.098 57.375 638 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.67 % Allowed : 26.37 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.35), residues: 574 helix: 1.46 (0.36), residues: 221 sheet: 1.56 (0.56), residues: 88 loop : 0.05 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 81 HIS 0.002 0.000 HIS E 309 PHE 0.018 0.002 PHE C 314 TYR 0.011 0.001 TYR C 278 ARG 0.003 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.540 Fit side-chains REVERT: E 174 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6795 (mmmt) REVERT: C 66 MET cc_start: 0.6772 (ttp) cc_final: 0.6317 (ttp) REVERT: C 114 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: C 300 MET cc_start: 0.8137 (mtt) cc_final: 0.7934 (mtp) outliers start: 23 outliers final: 13 residues processed: 84 average time/residue: 1.5192 time to fit residues: 131.8562 Evaluate side-chains 87 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 198 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 163 HIS E 275 HIS C 148 GLN C 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 4713 Z= 0.393 Angle : 0.631 8.503 6405 Z= 0.314 Chirality : 0.044 0.150 733 Planarity : 0.005 0.034 840 Dihedral : 6.134 58.771 635 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.06 % Allowed : 25.35 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.34), residues: 574 helix: 1.03 (0.35), residues: 220 sheet: 2.12 (0.56), residues: 79 loop : -0.28 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.003 0.001 HIS C 275 PHE 0.026 0.003 PHE C 314 TYR 0.017 0.002 TYR C 278 ARG 0.003 0.001 ARG C 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.536 Fit side-chains REVERT: E 116 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7627 (ptmm) REVERT: E 166 GLU cc_start: 0.6953 (pm20) cc_final: 0.6595 (pm20) REVERT: E 312 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: C 83 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: C 114 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: C 272 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7462 (mp0) outliers start: 20 outliers final: 10 residues processed: 86 average time/residue: 1.5978 time to fit residues: 141.6749 Evaluate side-chains 88 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 338 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 0.0570 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4713 Z= 0.219 Angle : 0.529 8.002 6405 Z= 0.261 Chirality : 0.039 0.147 733 Planarity : 0.004 0.031 840 Dihedral : 5.781 56.487 635 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.26 % Allowed : 25.15 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.34), residues: 574 helix: 1.21 (0.35), residues: 220 sheet: 1.45 (0.55), residues: 88 loop : -0.09 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 81 HIS 0.003 0.001 HIS E 309 PHE 0.022 0.002 PHE C 314 TYR 0.012 0.002 TYR C 278 ARG 0.007 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.662 Fit side-chains REVERT: E 116 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7592 (ptmm) REVERT: E 159 LEU cc_start: 0.8240 (mt) cc_final: 0.8032 (mp) REVERT: E 166 GLU cc_start: 0.6920 (pm20) cc_final: 0.6597 (pm20) REVERT: E 174 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6773 (mmmt) REVERT: C 114 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: C 272 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7447 (mp0) outliers start: 21 outliers final: 11 residues processed: 89 average time/residue: 1.5495 time to fit residues: 142.2472 Evaluate side-chains 88 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 148 GLN C 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4713 Z= 0.366 Angle : 0.617 9.054 6405 Z= 0.305 Chirality : 0.043 0.148 733 Planarity : 0.004 0.033 840 Dihedral : 5.909 59.433 635 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.67 % Allowed : 24.95 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.34), residues: 574 helix: 0.96 (0.35), residues: 220 sheet: 1.75 (0.55), residues: 83 loop : -0.30 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 81 HIS 0.003 0.001 HIS E 309 PHE 0.025 0.003 PHE C 314 TYR 0.016 0.002 TYR C 278 ARG 0.008 0.001 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.532 Fit side-chains REVERT: E 159 LEU cc_start: 0.8301 (mt) cc_final: 0.8088 (mp) REVERT: E 166 GLU cc_start: 0.6856 (pm20) cc_final: 0.6472 (pm20) REVERT: C 114 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: C 272 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7531 (mp0) outliers start: 23 outliers final: 14 residues processed: 87 average time/residue: 1.4766 time to fit residues: 132.6904 Evaluate side-chains 90 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4713 Z= 0.173 Angle : 0.502 7.921 6405 Z= 0.249 Chirality : 0.038 0.148 733 Planarity : 0.004 0.030 840 Dihedral : 5.431 56.860 635 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.65 % Allowed : 26.37 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.34), residues: 574 helix: 1.29 (0.35), residues: 220 sheet: 1.35 (0.54), residues: 88 loop : -0.04 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 81 HIS 0.003 0.001 HIS E 309 PHE 0.020 0.002 PHE C 314 TYR 0.009 0.001 TYR C 278 ARG 0.008 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.550 Fit side-chains REVERT: E 166 GLU cc_start: 0.6879 (pm20) cc_final: 0.6657 (pm20) REVERT: E 174 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6763 (mmmt) REVERT: C 114 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: C 272 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7499 (mp0) outliers start: 18 outliers final: 10 residues processed: 91 average time/residue: 1.4960 time to fit residues: 140.6036 Evaluate side-chains 90 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.0570 chunk 48 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 25 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 124 GLN C 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4713 Z= 0.139 Angle : 0.502 9.332 6405 Z= 0.243 Chirality : 0.038 0.146 733 Planarity : 0.003 0.031 840 Dihedral : 5.190 55.727 635 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.85 % Allowed : 26.17 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.34), residues: 574 helix: 1.41 (0.36), residues: 221 sheet: 1.23 (0.54), residues: 88 loop : 0.05 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 81 HIS 0.002 0.000 HIS E 309 PHE 0.017 0.002 PHE C 314 TYR 0.008 0.001 TYR C 278 ARG 0.007 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.532 Fit side-chains REVERT: E 166 GLU cc_start: 0.6908 (pm20) cc_final: 0.6587 (pm20) REVERT: E 174 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6739 (mmmt) REVERT: C 114 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: C 272 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: C 300 MET cc_start: 0.8121 (mtt) cc_final: 0.7910 (mtp) outliers start: 19 outliers final: 10 residues processed: 89 average time/residue: 1.6130 time to fit residues: 148.2480 Evaluate side-chains 91 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 124 GLN C 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4713 Z= 0.145 Angle : 0.483 6.180 6405 Z= 0.240 Chirality : 0.038 0.144 733 Planarity : 0.003 0.034 840 Dihedral : 4.984 56.723 633 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.25 % Allowed : 26.98 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.35), residues: 574 helix: 1.50 (0.36), residues: 221 sheet: 1.22 (0.55), residues: 88 loop : 0.08 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 81 HIS 0.001 0.000 HIS E 309 PHE 0.017 0.002 PHE C 314 TYR 0.009 0.001 TYR C 278 ARG 0.008 0.000 ARG C 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.533 Fit side-chains REVERT: E 166 GLU cc_start: 0.6913 (pm20) cc_final: 0.6636 (pm20) REVERT: E 174 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6708 (mmmt) REVERT: E 233 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6809 (ttm170) REVERT: C 66 MET cc_start: 0.6787 (ttp) cc_final: 0.6335 (ttp) REVERT: C 114 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: C 272 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7467 (mp0) outliers start: 16 outliers final: 8 residues processed: 85 average time/residue: 1.5231 time to fit residues: 133.7046 Evaluate side-chains 86 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN E 275 HIS C 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.177960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.134624 restraints weight = 4578.285| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.26 r_work: 0.3095 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4713 Z= 0.195 Angle : 0.537 7.397 6405 Z= 0.258 Chirality : 0.039 0.144 733 Planarity : 0.004 0.030 840 Dihedral : 5.111 58.833 633 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.25 % Allowed : 27.59 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.34), residues: 574 helix: 1.46 (0.36), residues: 221 sheet: 1.26 (0.54), residues: 88 loop : 0.04 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 81 HIS 0.002 0.001 HIS E 309 PHE 0.020 0.002 PHE C 314 TYR 0.011 0.001 TYR C 278 ARG 0.008 0.000 ARG C 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2803.31 seconds wall clock time: 50 minutes 35.68 seconds (3035.68 seconds total)