Starting phenix.real_space_refine on Thu Jul 2 05:41:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eq4_28535/07_2026/8eq4_28535.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eq4_28535/07_2026/8eq4_28535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8eq4_28535/07_2026/8eq4_28535.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eq4_28535/07_2026/8eq4_28535.cif" model { file = "/net/cci-nas-00/data/ceres_data/8eq4_28535/07_2026/8eq4_28535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eq4_28535/07_2026/8eq4_28535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eq4_28535/07_2026/8eq4_28535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eq4_28535/07_2026/8eq4_28535.map" } resolution = 2.71 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= 0.003 sd= 0.022 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 33 5.16 5 C 4485 2.51 5 N 1119 2.21 5 O 1263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6903 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2217 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {'NAG': 4, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 10 Restraints were copied for chains: B, C Time building chain proxies: 1.04, per 1000 atoms: 0.15 Number of scatterers: 6903 At special positions: 0 Unit cell: (80.122, 81.774, 124.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 3 15.00 O 1263 8.00 N 1119 7.00 C 4485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG A 404 " - " ASN A 155 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG B 404 " - " ASN B 155 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG C 404 " - " ASN C 155 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 312.9 milliseconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 37.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 57 through 94 Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.676A pdb=" N PHE A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.191A pdb=" N SER A 277 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.817A pdb=" N ASN A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 302' Processing helix chain 'A' and resid 302 through 339 removed outlier: 4.148A pdb=" N THR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 94 Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.676A pdb=" N PHE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.191A pdb=" N SER B 277 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.818A pdb=" N ASN B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 302' Processing helix chain 'B' and resid 302 through 339 removed outlier: 4.147A pdb=" N THR B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 329 " --> pdb=" O LYS B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 94 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.677A pdb=" N PHE C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 226 Processing helix chain 'C' and resid 272 through 278 removed outlier: 4.190A pdb=" N SER C 277 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.817A pdb=" N ASN C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 302 through 339 removed outlier: 4.148A pdb=" N THR C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 329 " --> pdb=" O LYS C 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 100 through 107 current: chain 'A' and resid 181 through 189 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 181 through 189 current: chain 'A' and resid 254 through 259 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 254 through 259 current: chain 'B' and resid 181 through 189 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 181 through 189 current: chain 'B' and resid 254 through 259 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 254 through 259 current: chain 'C' and resid 181 through 189 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 181 through 189 current: chain 'C' and resid 254 through 259 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 157 removed outlier: 3.644A pdb=" N GLY A 115 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 199 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 232 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 157 removed outlier: 3.643A pdb=" N GLY B 115 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 199 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 232 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.643A pdb=" N GLY C 115 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 199 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 232 " --> pdb=" O ILE C 199 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 822 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: 0.68 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1082 1.32 - 1.44: 1986 1.44 - 1.56: 3946 1.56 - 1.69: 6 1.69 - 1.81: 51 Bond restraints: 7071 Sorted by residual: bond pdb=" O1 PIO C 405 " pdb=" P1 PIO C 405 " ideal model delta sigma weight residual 1.633 1.478 0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" O1 PIO B 405 " pdb=" P1 PIO B 405 " ideal model delta sigma weight residual 1.633 1.478 0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" O1 PIO A 405 " pdb=" P1 PIO A 405 " ideal model delta sigma weight residual 1.633 1.479 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" O11 PIO C 405 " pdb=" P1 PIO C 405 " ideal model delta sigma weight residual 1.495 1.566 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" O11 PIO A 405 " pdb=" P1 PIO A 405 " ideal model delta sigma weight residual 1.495 1.566 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 7066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 9558 4.06 - 8.12: 15 8.12 - 12.18: 6 12.18 - 16.25: 3 16.25 - 20.31: 3 Bond angle restraints: 9585 Sorted by residual: angle pdb=" O11 PIO C 405 " pdb=" P1 PIO C 405 " pdb=" O12 PIO C 405 " ideal model delta sigma weight residual 121.09 100.78 20.31 3.00e+00 1.11e-01 4.58e+01 angle pdb=" O11 PIO B 405 " pdb=" P1 PIO B 405 " pdb=" O12 PIO B 405 " ideal model delta sigma weight residual 121.09 100.83 20.26 3.00e+00 1.11e-01 4.56e+01 angle pdb=" O11 PIO A 405 " pdb=" P1 PIO A 405 " pdb=" O12 PIO A 405 " ideal model delta sigma weight residual 121.09 100.84 20.25 3.00e+00 1.11e-01 4.56e+01 angle pdb=" C ARG B 93 " pdb=" CA ARG B 93 " pdb=" CB ARG B 93 " ideal model delta sigma weight residual 110.90 104.03 6.87 1.58e+00 4.01e-01 1.89e+01 angle pdb=" C ARG C 93 " pdb=" CA ARG C 93 " pdb=" CB ARG C 93 " ideal model delta sigma weight residual 110.90 104.04 6.86 1.58e+00 4.01e-01 1.89e+01 ... (remaining 9580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 3745 15.69 - 31.38: 275 31.38 - 47.07: 72 47.07 - 62.76: 9 62.76 - 78.45: 9 Dihedral angle restraints: 4110 sinusoidal: 1596 harmonic: 2514 Sorted by residual: dihedral pdb=" CA PHE A 204 " pdb=" C PHE A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta harmonic sigma weight residual 180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" CA PHE C 204 " pdb=" C PHE C 204 " pdb=" N SER C 205 " pdb=" CA SER C 205 " ideal model delta harmonic sigma weight residual -180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.78e+00 dihedral pdb=" CA PHE B 204 " pdb=" C PHE B 204 " pdb=" N SER B 205 " pdb=" CA SER B 205 " ideal model delta harmonic sigma weight residual -180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.77e+00 ... (remaining 4107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 937 0.058 - 0.116: 146 0.116 - 0.175: 9 0.175 - 0.233: 0 0.233 - 0.291: 6 Chirality restraints: 1098 Sorted by residual: chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 148 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1095 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 403 " 0.304 2.00e-02 2.50e+03 2.57e-01 8.29e+02 pdb=" C7 NAG A 403 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG A 403 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A 403 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG A 403 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " -0.304 2.00e-02 2.50e+03 2.57e-01 8.28e+02 pdb=" C7 NAG C 403 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " 0.445 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 403 " -0.303 2.00e-02 2.50e+03 2.57e-01 8.27e+02 pdb=" C7 NAG B 403 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 403 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG B 403 " 0.445 2.00e-02 2.50e+03 pdb=" O7 NAG B 403 " -0.035 2.00e-02 2.50e+03 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1107 2.77 - 3.30: 6693 3.30 - 3.83: 11273 3.83 - 4.37: 12946 4.37 - 4.90: 22878 Nonbonded interactions: 54897 Sorted by model distance: nonbonded pdb=" OH TYR B 119 " pdb=" OE2 GLU B 224 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 119 " pdb=" OE2 GLU A 224 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR C 119 " pdb=" OE2 GLU C 224 " model vdw 2.233 3.040 nonbonded pdb=" ND2 ASN C 302 " pdb=" OD1 ASN C 305 " model vdw 2.363 3.120 nonbonded pdb=" ND2 ASN A 302 " pdb=" OD1 ASN A 305 " model vdw 2.364 3.120 ... (remaining 54892 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.50 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.380 Find NCS groups from input model: 0.050 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:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 : 0.006 0.155 7086 Z= 0.285 Angle : 0.793 20.307 9627 Z= 0.338 Chirality : 0.047 0.291 1098 Planarity : 0.020 0.257 1191 Dihedral : 12.415 78.450 2463 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.28 (0.29), residues: 843 helix: 3.09 (0.26), residues: 315 sheet: -0.31 (0.29), residues: 330 loop : -0.66 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.008 0.001 TYR C 86 PHE 0.011 0.001 PHE A 204 TRP 0.014 0.001 TRP A 330 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.28 ( 7071) covalent geometry : angle 0.74428 / 0.33 ( 9585) SS BOND : bond 0.00130 / 0.07 ( 3) SS BOND : angle 0.14306 / 0.08 ( 6) hydrogen bonds : bond 0.13901 / 9.65 ( 283) hydrogen bonds : angle 5.18101 / 3.60 ( 822) link_NAG-ASN : bond 0.01063 / 0.76 ( 12) link_NAG-ASN : angle 4.55903 / 3.84 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.197 Fit side-chains REVERT: A 92 PHE cc_start: 0.8210 (t80) cc_final: 0.7891 (t80) REVERT: A 326 LEU cc_start: 0.8347 (tt) cc_final: 0.8010 (tt) REVERT: B 92 PHE cc_start: 0.8231 (t80) cc_final: 0.8028 (t80) REVERT: B 326 LEU cc_start: 0.8341 (tt) cc_final: 0.8014 (tt) REVERT: C 76 LEU cc_start: 0.8776 (tp) cc_final: 0.8574 (mp) REVERT: C 92 PHE cc_start: 0.8201 (t80) cc_final: 0.7998 (t80) REVERT: C 158 ASP cc_start: 0.8752 (t0) cc_final: 0.8529 (t0) REVERT: C 326 LEU cc_start: 0.8332 (tt) cc_final: 0.8003 (tt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.4375 time to fit residues: 68.9920 Evaluate side-chains 88 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 305 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.092107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.067306 restraints weight = 13873.601| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.31 r_work: 0.2782 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7086 Z= 0.145 Angle : 0.631 11.721 9627 Z= 0.291 Chirality : 0.046 0.304 1098 Planarity : 0.003 0.024 1191 Dihedral : 7.578 55.008 954 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.30 % Allowed : 11.26 % Favored : 87.45 % 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: 1.54 (0.29), residues: 843 helix: 3.47 (0.25), residues: 291 sheet: -0.35 (0.28), residues: 339 loop : 0.00 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 253 TYR 0.014 0.001 TYR A 86 PHE 0.015 0.001 PHE A 204 TRP 0.005 0.001 TRP B 304 HIS 0.001 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7071) covalent geometry : angle 0.55765 / 0.27 ( 9585) SS BOND : bond 0.00066 / 0.03 ( 3) SS BOND : angle 0.21549 / 0.12 ( 6) hydrogen bonds : bond 0.03446 / 2.40 ( 283) hydrogen bonds : angle 4.19416 / 2.93 ( 822) link_NAG-ASN : bond 0.01057 / 0.76 ( 12) link_NAG-ASN : angle 4.87869 / 4.05 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.202 Fit side-chains REVERT: A 92 PHE cc_start: 0.8324 (t80) cc_final: 0.8107 (t80) REVERT: A 158 ASP cc_start: 0.8616 (t0) cc_final: 0.8351 (t0) REVERT: B 92 PHE cc_start: 0.8313 (t80) cc_final: 0.7996 (t80) REVERT: B 176 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: C 92 PHE cc_start: 0.8245 (t80) cc_final: 0.7907 (t80) outliers start: 9 outliers final: 4 residues processed: 103 average time/residue: 0.2717 time to fit residues: 30.8040 Evaluate side-chains 91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain C residue 325 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.0020 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066730 restraints weight = 13765.859| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.28 r_work: 0.2786 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7086 Z= 0.114 Angle : 0.597 11.712 9627 Z= 0.269 Chirality : 0.045 0.303 1098 Planarity : 0.002 0.014 1191 Dihedral : 7.162 56.034 954 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.15 % Allowed : 12.12 % Favored : 86.72 % 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: 1.59 (0.29), residues: 843 helix: 3.44 (0.25), residues: 294 sheet: -0.41 (0.28), residues: 333 loop : 0.26 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.012 0.001 TYR A 227 PHE 0.025 0.001 PHE C 83 TRP 0.004 0.001 TRP C 230 HIS 0.001 0.000 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 7071) covalent geometry : angle 0.51897 / 0.25 ( 9585) SS BOND : bond 0.00028 / 0.01 ( 3) SS BOND : angle 0.26147 / 0.15 ( 6) hydrogen bonds : bond 0.03150 / 2.22 ( 283) hydrogen bonds : angle 3.87411 / 2.70 ( 822) link_NAG-ASN : bond 0.00979 / 0.71 ( 12) link_NAG-ASN : angle 4.86245 / 4.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.258 Fit side-chains REVERT: A 92 PHE cc_start: 0.8302 (t80) cc_final: 0.8017 (t80) REVERT: A 158 ASP cc_start: 0.8630 (t0) cc_final: 0.8425 (t0) REVERT: B 92 PHE cc_start: 0.8281 (t80) cc_final: 0.7985 (t80) REVERT: C 92 PHE cc_start: 0.8239 (t80) cc_final: 0.7895 (t80) outliers start: 8 outliers final: 1 residues processed: 96 average time/residue: 0.2453 time to fit residues: 25.9766 Evaluate side-chains 87 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.066203 restraints weight = 13872.687| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.33 r_work: 0.2758 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7086 Z= 0.133 Angle : 0.585 10.999 9627 Z= 0.264 Chirality : 0.045 0.312 1098 Planarity : 0.002 0.015 1191 Dihedral : 7.046 57.723 954 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.59 % Allowed : 13.42 % Favored : 84.99 % 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: 1.62 (0.29), residues: 843 helix: 3.50 (0.25), residues: 294 sheet: -0.48 (0.28), residues: 333 loop : 0.37 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 253 TYR 0.011 0.001 TYR A 227 PHE 0.015 0.001 PHE A 204 TRP 0.005 0.001 TRP C 304 HIS 0.001 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7071) covalent geometry : angle 0.51384 / 0.25 ( 9585) SS BOND : bond 0.00035 / 0.02 ( 3) SS BOND : angle 0.28120 / 0.16 ( 6) hydrogen bonds : bond 0.03087 / 2.16 ( 283) hydrogen bonds : angle 3.70613 / 2.59 ( 822) link_NAG-ASN : bond 0.00962 / 0.69 ( 12) link_NAG-ASN : angle 4.60192 / 3.87 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.281 Fit side-chains REVERT: A 92 PHE cc_start: 0.8265 (t80) cc_final: 0.7995 (t80) REVERT: A 251 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8436 (p0) REVERT: B 92 PHE cc_start: 0.8280 (t80) cc_final: 0.7977 (t80) REVERT: B 251 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8470 (p0) REVERT: C 92 PHE cc_start: 0.8216 (t80) cc_final: 0.7927 (t80) REVERT: C 251 ASP cc_start: 0.8922 (p0) cc_final: 0.8512 (p0) outliers start: 11 outliers final: 2 residues processed: 92 average time/residue: 0.2361 time to fit residues: 24.3211 Evaluate side-chains 89 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 251 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.089190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.064130 restraints weight = 14010.875| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.32 r_work: 0.2714 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7086 Z= 0.186 Angle : 0.599 10.395 9627 Z= 0.277 Chirality : 0.045 0.313 1098 Planarity : 0.003 0.018 1191 Dihedral : 7.174 59.827 954 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.03 % Allowed : 12.99 % Favored : 83.98 % 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: 1.51 (0.29), residues: 843 helix: 3.39 (0.25), residues: 297 sheet: -0.63 (0.27), residues: 333 loop : 0.48 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 110 TYR 0.014 0.001 TYR B 227 PHE 0.030 0.002 PHE C 83 TRP 0.007 0.001 TRP B 304 HIS 0.001 0.000 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 7071) covalent geometry : angle 0.53706 / 0.26 ( 9585) SS BOND : bond 0.00049 / 0.02 ( 3) SS BOND : angle 0.49324 / 0.28 ( 6) hydrogen bonds : bond 0.03257 / 2.27 ( 283) hydrogen bonds : angle 3.72156 / 2.62 ( 822) link_NAG-ASN : bond 0.00924 / 0.67 ( 12) link_NAG-ASN : angle 4.35751 / 3.67 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8280 (mp) REVERT: A 92 PHE cc_start: 0.8268 (t80) cc_final: 0.8033 (t80) REVERT: A 158 ASP cc_start: 0.8678 (t0) cc_final: 0.8446 (t0) REVERT: A 251 ASP cc_start: 0.8892 (p0) cc_final: 0.8424 (p0) REVERT: B 92 PHE cc_start: 0.8289 (t80) cc_final: 0.7976 (t80) REVERT: B 158 ASP cc_start: 0.8667 (t0) cc_final: 0.8448 (t0) REVERT: B 251 ASP cc_start: 0.8905 (p0) cc_final: 0.8479 (p0) REVERT: C 92 PHE cc_start: 0.8221 (t80) cc_final: 0.7945 (t80) REVERT: C 251 ASP cc_start: 0.8883 (p0) cc_final: 0.8503 (p0) outliers start: 21 outliers final: 10 residues processed: 99 average time/residue: 0.2281 time to fit residues: 25.3735 Evaluate side-chains 96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 0.0770 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 ASN B 266 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.065318 restraints weight = 13965.995| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.32 r_work: 0.2731 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7086 Z= 0.121 Angle : 0.594 11.204 9627 Z= 0.268 Chirality : 0.045 0.310 1098 Planarity : 0.002 0.018 1191 Dihedral : 7.052 59.864 954 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.73 % Allowed : 14.86 % Favored : 83.41 % 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: 1.58 (0.29), residues: 843 helix: 3.53 (0.25), residues: 294 sheet: -0.62 (0.27), residues: 333 loop : 0.49 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 253 TYR 0.013 0.001 TYR B 227 PHE 0.015 0.001 PHE A 204 TRP 0.005 0.001 TRP C 304 HIS 0.001 0.000 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 7071) covalent geometry : angle 0.52967 / 0.25 ( 9585) SS BOND : bond 0.00020 / 0.01 ( 3) SS BOND : angle 0.34577 / 0.19 ( 6) hydrogen bonds : bond 0.03094 / 2.15 ( 283) hydrogen bonds : angle 3.62775 / 2.54 ( 822) link_NAG-ASN : bond 0.00910 / 0.66 ( 12) link_NAG-ASN : angle 4.44836 / 3.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8264 (mp) REVERT: A 92 PHE cc_start: 0.8271 (t80) cc_final: 0.8044 (t80) REVERT: A 158 ASP cc_start: 0.8645 (t0) cc_final: 0.8406 (t0) REVERT: A 251 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8434 (p0) REVERT: B 92 PHE cc_start: 0.8262 (t80) cc_final: 0.7932 (t80) REVERT: B 158 ASP cc_start: 0.8660 (t0) cc_final: 0.8418 (t0) REVERT: B 251 ASP cc_start: 0.8886 (p0) cc_final: 0.8476 (p0) REVERT: C 92 PHE cc_start: 0.8224 (t80) cc_final: 0.7932 (t80) REVERT: C 251 ASP cc_start: 0.8858 (p0) cc_final: 0.8507 (p0) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.1930 time to fit residues: 20.4168 Evaluate side-chains 95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 34 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 ASN C 266 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.065287 restraints weight = 13819.470| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.30 r_work: 0.2747 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7086 Z= 0.111 Angle : 0.593 10.703 9627 Z= 0.266 Chirality : 0.044 0.309 1098 Planarity : 0.002 0.017 1191 Dihedral : 6.886 59.670 954 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.02 % Allowed : 15.58 % Favored : 82.40 % 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: 1.60 (0.29), residues: 843 helix: 3.50 (0.25), residues: 297 sheet: -0.63 (0.27), residues: 333 loop : 0.56 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 110 TYR 0.014 0.001 TYR B 227 PHE 0.031 0.001 PHE C 83 TRP 0.004 0.001 TRP C 304 HIS 0.001 0.000 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7071) covalent geometry : angle 0.53162 / 0.25 ( 9585) SS BOND : bond 0.00010 / 0.00 ( 3) SS BOND : angle 0.28926 / 0.16 ( 6) hydrogen bonds : bond 0.03016 / 2.11 ( 283) hydrogen bonds : angle 3.58093 / 2.50 ( 822) link_NAG-ASN : bond 0.00917 / 0.66 ( 12) link_NAG-ASN : angle 4.32289 / 3.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8255 (mp) REVERT: A 92 PHE cc_start: 0.8278 (t80) cc_final: 0.8060 (t80) REVERT: A 158 ASP cc_start: 0.8669 (t0) cc_final: 0.8384 (t0) REVERT: A 251 ASP cc_start: 0.8894 (p0) cc_final: 0.8455 (p0) REVERT: B 92 PHE cc_start: 0.8249 (t80) cc_final: 0.7927 (t80) REVERT: B 158 ASP cc_start: 0.8714 (t0) cc_final: 0.8471 (t0) REVERT: B 251 ASP cc_start: 0.8876 (p0) cc_final: 0.8501 (p0) REVERT: C 92 PHE cc_start: 0.8227 (t80) cc_final: 0.7943 (t80) REVERT: C 251 ASP cc_start: 0.8856 (p0) cc_final: 0.8500 (p0) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.1677 time to fit residues: 18.6332 Evaluate side-chains 95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.0000 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 75 optimal weight: 0.0070 chunk 43 optimal weight: 0.7980 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.091549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.066704 restraints weight = 13942.626| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.32 r_work: 0.2769 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7086 Z= 0.098 Angle : 0.589 10.149 9627 Z= 0.264 Chirality : 0.044 0.307 1098 Planarity : 0.002 0.016 1191 Dihedral : 6.737 59.814 954 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.44 % Allowed : 16.88 % Favored : 81.67 % 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: 1.62 (0.29), residues: 843 helix: 3.54 (0.25), residues: 297 sheet: -0.61 (0.28), residues: 333 loop : 0.53 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 253 TYR 0.014 0.001 TYR B 227 PHE 0.014 0.001 PHE A 204 TRP 0.004 0.000 TRP A 230 HIS 0.001 0.000 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 7071) covalent geometry : angle 0.52962 / 0.25 ( 9585) SS BOND : bond 0.00005 / 0.00 ( 3) SS BOND : angle 0.24952 / 0.14 ( 6) hydrogen bonds : bond 0.02962 / 2.07 ( 283) hydrogen bonds : angle 3.53279 / 2.46 ( 822) link_NAG-ASN : bond 0.00917 / 0.66 ( 12) link_NAG-ASN : angle 4.25112 / 3.58 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 92 PHE cc_start: 0.8253 (t80) cc_final: 0.8033 (t80) REVERT: A 158 ASP cc_start: 0.8654 (t0) cc_final: 0.8440 (t0) REVERT: A 251 ASP cc_start: 0.8888 (p0) cc_final: 0.8460 (p0) REVERT: B 92 PHE cc_start: 0.8243 (t80) cc_final: 0.7917 (t80) REVERT: B 158 ASP cc_start: 0.8675 (t0) cc_final: 0.8438 (t0) REVERT: B 251 ASP cc_start: 0.8848 (p0) cc_final: 0.8478 (p0) REVERT: C 92 PHE cc_start: 0.8204 (t80) cc_final: 0.7850 (t80) REVERT: C 251 ASP cc_start: 0.8866 (p0) cc_final: 0.8514 (p0) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.2002 time to fit residues: 21.6276 Evaluate side-chains 92 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.090450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.065684 restraints weight = 13940.360| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.32 r_work: 0.2752 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7086 Z= 0.121 Angle : 0.605 10.658 9627 Z= 0.270 Chirality : 0.045 0.313 1098 Planarity : 0.002 0.016 1191 Dihedral : 6.701 59.949 954 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.73 % Allowed : 16.74 % Favored : 81.53 % 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: 1.60 (0.29), residues: 843 helix: 3.53 (0.25), residues: 297 sheet: -0.63 (0.27), residues: 333 loop : 0.53 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 110 TYR 0.014 0.001 TYR B 227 PHE 0.031 0.001 PHE C 83 TRP 0.004 0.000 TRP A 304 HIS 0.001 0.000 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7071) covalent geometry : angle 0.55027 / 0.26 ( 9585) SS BOND : bond 0.00014 / 0.01 ( 3) SS BOND : angle 0.23873 / 0.14 ( 6) hydrogen bonds : bond 0.03060 / 2.14 ( 283) hydrogen bonds : angle 3.56630 / 2.49 ( 822) link_NAG-ASN : bond 0.00887 / 0.64 ( 12) link_NAG-ASN : angle 4.16256 / 3.51 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8280 (mp) REVERT: A 92 PHE cc_start: 0.8285 (t80) cc_final: 0.8058 (t80) REVERT: A 158 ASP cc_start: 0.8641 (t0) cc_final: 0.8399 (t0) REVERT: A 251 ASP cc_start: 0.8875 (p0) cc_final: 0.8474 (p0) REVERT: B 92 PHE cc_start: 0.8215 (t80) cc_final: 0.7903 (t80) REVERT: B 158 ASP cc_start: 0.8680 (t0) cc_final: 0.8441 (t0) REVERT: B 251 ASP cc_start: 0.8804 (p0) cc_final: 0.8459 (p0) REVERT: C 92 PHE cc_start: 0.8220 (t80) cc_final: 0.7880 (t80) REVERT: C 251 ASP cc_start: 0.8869 (p0) cc_final: 0.8520 (p0) outliers start: 12 outliers final: 9 residues processed: 93 average time/residue: 0.2020 time to fit residues: 21.1618 Evaluate side-chains 91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 311 CYS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 0 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.066090 restraints weight = 13869.480| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.32 r_work: 0.2752 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7086 Z= 0.119 Angle : 0.599 10.994 9627 Z= 0.269 Chirality : 0.045 0.312 1098 Planarity : 0.002 0.016 1191 Dihedral : 6.654 59.839 954 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.59 % Allowed : 16.88 % Favored : 81.53 % 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: 1.56 (0.29), residues: 843 helix: 3.46 (0.25), residues: 297 sheet: -0.64 (0.27), residues: 333 loop : 0.54 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 110 TYR 0.014 0.001 TYR B 227 PHE 0.014 0.001 PHE A 204 TRP 0.004 0.000 TRP A 304 HIS 0.001 0.000 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7071) covalent geometry : angle 0.54446 / 0.26 ( 9585) SS BOND : bond 0.00018 / 0.01 ( 3) SS BOND : angle 0.22690 / 0.13 ( 6) hydrogen bonds : bond 0.03170 / 2.21 ( 283) hydrogen bonds : angle 3.53386 / 2.46 ( 822) link_NAG-ASN : bond 0.00886 / 0.64 ( 12) link_NAG-ASN : angle 4.13128 / 3.48 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8275 (mp) REVERT: A 92 PHE cc_start: 0.8271 (t80) cc_final: 0.8061 (t80) REVERT: A 251 ASP cc_start: 0.8854 (p0) cc_final: 0.8466 (p0) REVERT: B 92 PHE cc_start: 0.8223 (t80) cc_final: 0.7896 (t80) REVERT: B 158 ASP cc_start: 0.8690 (t0) cc_final: 0.8471 (t0) REVERT: B 251 ASP cc_start: 0.8799 (p0) cc_final: 0.8458 (p0) REVERT: C 92 PHE cc_start: 0.8210 (t80) cc_final: 0.7865 (t80) REVERT: C 251 ASP cc_start: 0.8861 (p0) cc_final: 0.8542 (p0) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.1872 time to fit residues: 19.5231 Evaluate side-chains 90 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 247 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.090423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.065585 restraints weight = 13923.671| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.32 r_work: 0.2754 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7086 Z= 0.120 Angle : 0.614 11.105 9627 Z= 0.274 Chirality : 0.045 0.313 1098 Planarity : 0.002 0.016 1191 Dihedral : 6.598 59.607 954 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.59 % Allowed : 16.88 % Favored : 81.53 % 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: 1.55 (0.29), residues: 843 helix: 3.43 (0.25), residues: 297 sheet: -0.64 (0.27), residues: 333 loop : 0.56 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 110 TYR 0.014 0.001 TYR B 227 PHE 0.032 0.001 PHE C 83 TRP 0.004 0.000 TRP A 304 HIS 0.001 0.000 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7071) covalent geometry : angle 0.56203 / 0.26 ( 9585) SS BOND : bond 0.00027 / 0.01 ( 3) SS BOND : angle 0.22631 / 0.13 ( 6) hydrogen bonds : bond 0.03131 / 2.18 ( 283) hydrogen bonds : angle 3.51570 / 2.45 ( 822) link_NAG-ASN : bond 0.00878 / 0.63 ( 12) link_NAG-ASN : angle 4.08464 / 3.44 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.46 seconds wall clock time: 32 minutes 14.42 seconds (1934.42 seconds total)