Starting phenix.real_space_refine on Tue Mar 3 12:45:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0t_26950/03_2026/7v0t_26950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0t_26950/03_2026/7v0t_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_26950/03_2026/7v0t_26950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0t_26950/03_2026/7v0t_26950.map" model { file = "/net/cci-nas-00/data/ceres_data/7v0t_26950/03_2026/7v0t_26950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0t_26950/03_2026/7v0t_26950.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS: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: 0.98, per 1000 atoms: 0.21 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: 0.25 Conformation dependent library (CDL) restraints added in 330.5 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: 0.09 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: 0.57 Time building geometry restraints manager: 0.38 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: 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: 1.890 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: 0.270 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.590 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:9.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- 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= 0.165 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG E 112 TYR 0.019 0.002 TYR E 278 PHE 0.022 0.002 PHE C 314 TRP 0.015 0.002 TRP E 81 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 4713) covalent geometry : angle 0.63087 ( 6405) hydrogen bonds : bond 0.15437 ( 164) hydrogen bonds : angle 5.85728 ( 468) *********************** 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 : 0.207 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: 0.8113 (mp0) outliers start: 17 outliers final: 12 residues processed: 84 average time/residue: 0.7423 time to fit residues: 64.3178 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 : 0.208 ------------------------------------------------------------------------------- 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 54 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 0.0010 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.0370 overall best weight: 1.5868 ------------------------------------------------------------------------------- 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 148 GLN C 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.177939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.136659 restraints weight = 4642.478| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.46 r_work: 0.3109 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0674 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= 0.121 Angle : 0.524 6.705 6405 Z= 0.260 Chirality : 0.039 0.152 733 Planarity : 0.004 0.029 840 Dihedral : 6.995 55.255 648 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.67 % Allowed : 25.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.34), residues: 574 helix: 1.10 (0.35), residues: 220 sheet: 1.89 (0.58), residues: 84 loop : -0.05 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 246 TYR 0.012 0.002 TYR E 278 PHE 0.019 0.002 PHE C 314 TRP 0.012 0.001 TRP E 81 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4713) covalent geometry : angle 0.52373 ( 6405) hydrogen bonds : bond 0.04041 ( 164) hydrogen bonds : angle 4.53687 ( 468) *********************** 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 93 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.164 Fit side-chains REVERT: E 63 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: C 114 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: C 233 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.8117 (mtt90) outliers start: 23 outliers final: 13 residues processed: 83 average time/residue: 0.7368 time to fit residues: 62.9628 Evaluate side-chains 83 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 GLU 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 73 LEU 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 126 THR 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 40 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.0060 overall best weight: 1.5200 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.178332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.133876 restraints weight = 4533.143| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.48 r_work: 0.3118 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0912 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= 0.113 Angle : 0.491 6.923 6405 Z= 0.244 Chirality : 0.038 0.148 733 Planarity : 0.003 0.030 840 Dihedral : 6.406 57.162 640 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.07 % Allowed : 25.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.34), residues: 574 helix: 1.33 (0.36), residues: 220 sheet: 1.91 (0.57), residues: 84 loop : -0.05 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 246 TYR 0.012 0.001 TYR E 278 PHE 0.019 0.002 PHE C 314 TRP 0.012 0.001 TRP E 81 HIS 0.002 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4713) covalent geometry : angle 0.49124 ( 6405) hydrogen bonds : bond 0.03749 ( 164) hydrogen bonds : angle 4.32272 ( 468) *********************** 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 97 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.158 Fit side-chains REVERT: E 312 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: C 114 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: C 233 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8232 (mtt90) REVERT: C 272 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7477 (mp0) outliers start: 25 outliers final: 13 residues processed: 86 average time/residue: 0.7195 time to fit residues: 63.7357 Evaluate side-chains 87 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 E residue 312 GLU 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 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 Chi-restraints excluded: chain C residue 272 GLU 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 33 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 148 GLN C 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.176638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135535 restraints weight = 4695.743| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.49 r_work: 0.3082 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4713 Z= 0.170 Angle : 0.558 7.896 6405 Z= 0.275 Chirality : 0.040 0.146 733 Planarity : 0.004 0.032 840 Dihedral : 6.464 58.395 638 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.67 % Allowed : 25.15 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.34), residues: 574 helix: 1.20 (0.35), residues: 220 sheet: 1.96 (0.57), residues: 84 loop : -0.13 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 112 TYR 0.015 0.002 TYR C 278 PHE 0.023 0.002 PHE C 314 TRP 0.014 0.002 TRP E 81 HIS 0.003 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4713) covalent geometry : angle 0.55778 ( 6405) hydrogen bonds : bond 0.04196 ( 164) hydrogen bonds : angle 4.36541 ( 468) *********************** 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 : 0.193 Fit side-chains REVERT: E 63 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: E 116 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7499 (ptmm) REVERT: E 125 GLU cc_start: 0.6435 (mm-30) cc_final: 0.6191 (mm-30) REVERT: C 83 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: C 114 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: C 233 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8187 (mtt90) REVERT: C 272 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7506 (mp0) outliers start: 23 outliers final: 13 residues processed: 86 average time/residue: 0.7654 time to fit residues: 67.7102 Evaluate side-chains 90 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE 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 C residue 72 GLU Chi-restraints excluded: chain C residue 83 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 11 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.0570 chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 overall best weight: 1.7900 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.177954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.135115 restraints weight = 4520.040| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.35 r_work: 0.3117 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1076 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= 0.122 Angle : 0.499 7.443 6405 Z= 0.248 Chirality : 0.038 0.146 733 Planarity : 0.003 0.030 840 Dihedral : 6.248 54.981 638 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.68 % Allowed : 24.75 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.34), residues: 574 helix: 1.37 (0.36), residues: 220 sheet: 1.88 (0.57), residues: 84 loop : -0.09 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 112 TYR 0.012 0.001 TYR C 278 PHE 0.020 0.002 PHE C 314 TRP 0.014 0.001 TRP E 81 HIS 0.002 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4713) covalent geometry : angle 0.49876 ( 6405) hydrogen bonds : bond 0.03681 ( 164) hydrogen bonds : angle 4.26279 ( 468) *********************** 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 104 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.169 Fit side-chains REVERT: E 63 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: E 116 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7562 (ptmm) REVERT: E 159 LEU cc_start: 0.8065 (mt) cc_final: 0.7799 (mp) REVERT: E 166 GLU cc_start: 0.6896 (pm20) cc_final: 0.6429 (pm20) REVERT: E 174 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6765 (mmmt) REVERT: C 83 GLN cc_start: 0.7520 (mt0) cc_final: 0.7103 (mp10) REVERT: C 114 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: C 233 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8260 (mtt90) REVERT: C 272 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7543 (mp0) outliers start: 28 outliers final: 16 residues processed: 93 average time/residue: 0.7024 time to fit residues: 67.2677 Evaluate side-chains 95 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE 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 109 GLU 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 Chi-restraints excluded: chain C residue 272 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.178706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.135026 restraints weight = 4594.782| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.49 r_work: 0.3093 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1172 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= 0.114 Angle : 0.493 7.183 6405 Z= 0.243 Chirality : 0.038 0.146 733 Planarity : 0.003 0.030 840 Dihedral : 6.095 55.671 638 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.48 % Allowed : 24.34 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.34), residues: 574 helix: 1.43 (0.36), residues: 220 sheet: 1.85 (0.57), residues: 84 loop : -0.02 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 112 TYR 0.012 0.001 TYR C 278 PHE 0.019 0.002 PHE C 314 TRP 0.013 0.001 TRP E 81 HIS 0.002 0.000 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4713) covalent geometry : angle 0.49271 ( 6405) hydrogen bonds : bond 0.03525 ( 164) hydrogen bonds : angle 4.20183 ( 468) *********************** 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 103 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.177 Fit side-chains REVERT: E 63 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: E 116 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7462 (ptmm) REVERT: E 159 LEU cc_start: 0.7993 (mt) cc_final: 0.7721 (mp) REVERT: E 166 GLU cc_start: 0.6895 (pm20) cc_final: 0.6469 (pm20) REVERT: E 174 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6733 (mmmt) REVERT: E 233 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6598 (mtm180) REVERT: C 83 GLN cc_start: 0.7468 (mt0) cc_final: 0.7095 (mp10) REVERT: C 114 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: C 233 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8160 (mtt90) REVERT: C 272 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7518 (mp0) outliers start: 27 outliers final: 15 residues processed: 92 average time/residue: 0.7358 time to fit residues: 69.6648 Evaluate side-chains 95 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE 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 109 GLU 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 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 6 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 0.0980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.177790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.134895 restraints weight = 4604.496| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.19 r_work: 0.3132 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1238 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= 0.110 Angle : 0.481 7.048 6405 Z= 0.238 Chirality : 0.038 0.145 733 Planarity : 0.003 0.030 840 Dihedral : 5.907 56.519 638 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.48 % Allowed : 24.95 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.34), residues: 574 helix: 1.50 (0.36), residues: 220 sheet: 1.88 (0.57), residues: 84 loop : 0.00 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 112 TYR 0.011 0.001 TYR C 278 PHE 0.019 0.002 PHE C 314 TRP 0.013 0.001 TRP E 81 HIS 0.002 0.000 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4713) covalent geometry : angle 0.48106 ( 6405) hydrogen bonds : bond 0.03447 ( 164) hydrogen bonds : angle 4.18198 ( 468) *********************** 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 102 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.184 Fit side-chains REVERT: E 63 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: E 116 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7557 (ptmm) REVERT: E 159 LEU cc_start: 0.8074 (mt) cc_final: 0.7808 (mp) REVERT: E 166 GLU cc_start: 0.6891 (pm20) cc_final: 0.6352 (pm20) REVERT: E 174 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6765 (mmmt) REVERT: E 233 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6615 (mtm180) REVERT: C 83 GLN cc_start: 0.7523 (mt0) cc_final: 0.7107 (mp10) REVERT: C 114 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: C 233 ARG cc_start: 0.8489 (mtm-85) cc_final: 0.8241 (mtt90) REVERT: C 272 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7552 (mp0) outliers start: 27 outliers final: 13 residues processed: 91 average time/residue: 0.6814 time to fit residues: 63.9305 Evaluate side-chains 91 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE 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 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 198 GLN 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 27 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.176043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135469 restraints weight = 4754.885| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.43 r_work: 0.3081 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4713 Z= 0.187 Angle : 0.566 8.064 6405 Z= 0.278 Chirality : 0.041 0.144 733 Planarity : 0.004 0.032 840 Dihedral : 5.379 59.451 633 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.67 % Allowed : 25.76 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.34), residues: 574 helix: 1.22 (0.35), residues: 220 sheet: 1.90 (0.57), residues: 84 loop : -0.09 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 112 TYR 0.015 0.002 TYR C 278 PHE 0.023 0.003 PHE C 314 TRP 0.013 0.002 TRP E 81 HIS 0.003 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 4713) covalent geometry : angle 0.56605 ( 6405) hydrogen bonds : bond 0.04243 ( 164) hydrogen bonds : angle 4.35685 ( 468) *********************** 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 100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.170 Fit side-chains REVERT: E 63 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: E 159 LEU cc_start: 0.8148 (mt) cc_final: 0.7894 (mp) REVERT: E 166 GLU cc_start: 0.6794 (pm20) cc_final: 0.6404 (pm20) REVERT: E 174 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6794 (mmmt) REVERT: E 233 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6744 (mtm180) REVERT: C 83 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: C 109 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: C 114 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: C 233 ARG cc_start: 0.8530 (mtm-85) cc_final: 0.8288 (mtt90) REVERT: C 272 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7588 (mp0) outliers start: 23 outliers final: 12 residues processed: 89 average time/residue: 0.6793 time to fit residues: 62.2952 Evaluate side-chains 94 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 63 GLU 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.177705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.134518 restraints weight = 4543.635| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.19 r_work: 0.3129 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1310 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= 0.108 Angle : 0.489 7.564 6405 Z= 0.241 Chirality : 0.038 0.145 733 Planarity : 0.003 0.030 840 Dihedral : 5.125 58.071 633 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.26 % Allowed : 26.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.34), residues: 574 helix: 1.46 (0.36), residues: 220 sheet: 1.88 (0.57), residues: 84 loop : 0.02 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 112 TYR 0.011 0.001 TYR C 278 PHE 0.020 0.002 PHE C 314 TRP 0.013 0.001 TRP E 81 HIS 0.002 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4713) covalent geometry : angle 0.48855 ( 6405) hydrogen bonds : bond 0.03493 ( 164) hydrogen bonds : angle 4.22952 ( 468) *********************** 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 99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.113 Fit side-chains REVERT: E 63 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7561 (mm-30) REVERT: E 116 LYS cc_start: 0.7599 (ptmm) cc_final: 0.7353 (ptmm) REVERT: E 159 LEU cc_start: 0.8068 (mt) cc_final: 0.7799 (mp) REVERT: E 166 GLU cc_start: 0.6807 (pm20) cc_final: 0.6499 (pm20) REVERT: E 174 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6752 (mmmt) REVERT: E 233 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6600 (mtm180) REVERT: C 66 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6390 (ttp) REVERT: C 83 GLN cc_start: 0.7545 (mt0) cc_final: 0.7032 (mp10) REVERT: C 109 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: C 114 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: C 233 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8232 (mtt90) REVERT: C 272 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7563 (mp0) outliers start: 21 outliers final: 10 residues processed: 89 average time/residue: 0.6733 time to fit residues: 61.7234 Evaluate side-chains 92 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 64 LEU 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 66 MET 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 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 38 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.177178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.136849 restraints weight = 4710.657| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.18 r_work: 0.3108 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4713 Z= 0.156 Angle : 0.541 7.724 6405 Z= 0.264 Chirality : 0.040 0.144 733 Planarity : 0.004 0.031 840 Dihedral : 5.267 59.839 633 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.06 % Allowed : 27.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.34), residues: 574 helix: 1.32 (0.35), residues: 220 sheet: 1.89 (0.57), residues: 84 loop : -0.05 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 112 TYR 0.013 0.002 TYR C 278 PHE 0.022 0.002 PHE C 314 TRP 0.013 0.001 TRP E 81 HIS 0.003 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4713) covalent geometry : angle 0.54118 ( 6405) hydrogen bonds : bond 0.03950 ( 164) hydrogen bonds : angle 4.27764 ( 468) ********************** 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 96 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.197 Fit side-chains REVERT: E 63 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: E 116 LYS cc_start: 0.7624 (ptmm) cc_final: 0.7383 (ptmm) REVERT: E 159 LEU cc_start: 0.8116 (mt) cc_final: 0.7853 (mp) REVERT: E 166 GLU cc_start: 0.6766 (pm20) cc_final: 0.6443 (pm20) REVERT: E 174 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6777 (mmmt) REVERT: E 233 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6652 (mtm180) REVERT: E 291 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: C 83 GLN cc_start: 0.7582 (mt0) cc_final: 0.7098 (mp10) REVERT: C 109 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: C 114 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: C 233 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8270 (mtt90) REVERT: C 272 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7642 (mp0) outliers start: 20 outliers final: 11 residues processed: 88 average time/residue: 0.7554 time to fit residues: 68.3403 Evaluate side-chains 92 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 64 LEU 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 E residue 291 GLU Chi-restraints excluded: chain E residue 312 GLU 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 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 1 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.176601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.135584 restraints weight = 4742.223| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.25 r_work: 0.3096 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4713 Z= 0.168 Angle : 0.549 8.066 6405 Z= 0.271 Chirality : 0.040 0.145 733 Planarity : 0.004 0.031 840 Dihedral : 5.323 59.027 633 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.46 % Allowed : 26.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.34), residues: 574 helix: 1.23 (0.35), residues: 220 sheet: 1.93 (0.57), residues: 84 loop : -0.11 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 112 TYR 0.014 0.002 TYR C 278 PHE 0.023 0.002 PHE C 314 TRP 0.013 0.002 TRP E 81 HIS 0.003 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4713) covalent geometry : angle 0.54918 ( 6405) hydrogen bonds : bond 0.04101 ( 164) hydrogen bonds : angle 4.32644 ( 468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2440.90 seconds wall clock time: 42 minutes 3.87 seconds (2523.87 seconds total)