Starting phenix.real_space_refine on Tue Aug 4 21:19:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11bc_75601/08_2026/11bc_75601.cif Found real_map, /net/cci-nas-00/data/ceres_data/11bc_75601/08_2026/11bc_75601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11bc_75601/08_2026/11bc_75601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11bc_75601/08_2026/11bc_75601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11bc_75601/08_2026/11bc_75601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11bc_75601/08_2026/11bc_75601.map" } resolution = 3.3 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= 0.004 sd= 0.017 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 16 5.16 5 C 4275 2.51 5 N 1214 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6793 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2318 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2315 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 539 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 58} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 543 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "F" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 535 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "E" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 543 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Time building chain proxies: 1.75, per 1000 atoms: 0.26 Number of scatterers: 6793 At special positions: 0 Unit cell: (105.78, 120.4, 83.42, 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 16 16.00 O 1288 8.00 N 1214 7.00 C 4275 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: 0.32 Conformation dependent library (CDL) restraints added in 391.1 milliseconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 5 sheets defined 57.4% alpha, 8.0% 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 55 through 60 removed outlier: 3.755A pdb=" N GLY A 58 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 71 through 122 removed outlier: 3.786A pdb=" N LYS A 94 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 137 through 155 removed outlier: 4.517A pdb=" N ILE A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.548A pdb=" N SER A 246 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 247' Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 313 through 333 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.685A pdb=" N GLY B 58 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 61 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 71 through 122 removed outlier: 3.800A pdb=" N LYS B 94 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 137 through 155 removed outlier: 4.451A pdb=" N ILE B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU B 153 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.562A pdb=" N MET B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.551A pdb=" N SER B 246 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 333 removed outlier: 4.228A pdb=" N LEU B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'C' and resid 8 through 25 Processing helix chain 'C' and resid 34 through 65 removed outlier: 3.506A pdb=" N ARG C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 25 Processing helix chain 'D' and resid 34 through 65 Processing helix chain 'F' and resid 9 through 24 Processing helix chain 'F' and resid 34 through 65 removed outlier: 3.750A pdb=" N ARG F 38 " --> pdb=" O THR F 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 25 Processing helix chain 'E' and resid 34 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 203 removed outlier: 3.673A pdb=" N ASP A 198 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 272 Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA4, first strand: chain 'B' and resid 196 through 203 removed outlier: 3.633A pdb=" N ASP B 198 " --> pdb=" O HIS B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 270 through 275 379 hydrogen bonds defined for protein. 1107 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: 0.66 Time building geometry restraints manager: 0.51 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: 2293 1.34 - 1.46: 1428 1.46 - 1.58: 3190 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 6935 Sorted by residual: bond pdb=" C ILE B 335 " pdb=" N PRO B 336 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.20e-02 6.94e+03 1.11e+01 bond pdb=" N LEU D 13 " pdb=" CA LEU D 13 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.21e-02 6.83e+03 5.16e+00 bond pdb=" N LEU E 13 " pdb=" CA LEU E 13 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.03e+00 bond pdb=" CB ASN A 267 " pdb=" CG ASN A 267 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.47e+00 bond pdb=" CB ASN B 267 " pdb=" CG ASN B 267 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.26e+00 ... (remaining 6930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 9055 1.98 - 3.96: 248 3.96 - 5.93: 39 5.93 - 7.91: 10 7.91 - 9.89: 5 Bond angle restraints: 9357 Sorted by residual: angle pdb=" CA ILE C 59 " pdb=" CB ILE C 59 " pdb=" CG1 ILE C 59 " ideal model delta sigma weight residual 110.40 118.29 -7.89 1.70e+00 3.46e-01 2.15e+01 angle pdb=" CA MET A 253 " pdb=" CB MET A 253 " pdb=" CG MET A 253 " ideal model delta sigma weight residual 114.10 122.90 -8.80 2.00e+00 2.50e-01 1.93e+01 angle pdb=" CA ASN A 267 " pdb=" CB ASN A 267 " pdb=" CG ASN A 267 " ideal model delta sigma weight residual 112.60 116.87 -4.27 1.00e+00 1.00e+00 1.82e+01 angle pdb=" C ALA B 318 " pdb=" N ILE B 319 " pdb=" CA ILE B 319 " ideal model delta sigma weight residual 120.60 125.70 -5.10 1.29e+00 6.01e-01 1.56e+01 angle pdb=" CA ASN B 267 " pdb=" CB ASN B 267 " pdb=" CG ASN B 267 " ideal model delta sigma weight residual 112.60 116.52 -3.92 1.00e+00 1.00e+00 1.54e+01 ... (remaining 9352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3665 17.35 - 34.69: 494 34.69 - 52.04: 115 52.04 - 69.38: 14 69.38 - 86.73: 7 Dihedral angle restraints: 4295 sinusoidal: 1861 harmonic: 2434 Sorted by residual: dihedral pdb=" CA GLU B 317 " pdb=" C GLU B 317 " pdb=" N ALA B 318 " pdb=" CA ALA B 318 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ASP D 7 " pdb=" CB ASP D 7 " pdb=" CG ASP D 7 " pdb=" OD1 ASP D 7 " ideal model delta sinusoidal sigma weight residual -30.00 -89.16 59.16 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA PHE A 298 " pdb=" C PHE A 298 " pdb=" N ASN A 299 " pdb=" CA ASN A 299 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 764 0.050 - 0.100: 183 0.100 - 0.150: 42 0.150 - 0.200: 5 0.200 - 0.250: 1 Chirality restraints: 995 Sorted by residual: chirality pdb=" CA ASP F 9 " pdb=" N ASP F 9 " pdb=" C ASP F 9 " pdb=" CB ASP F 9 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA GLN B 111 " pdb=" N GLN B 111 " pdb=" C GLN B 111 " pdb=" CB GLN B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA GLN A 111 " pdb=" N GLN A 111 " pdb=" C GLN A 111 " pdb=" CB GLN A 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 992 not shown) Planarity restraints: 1241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP F 9 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.49e+01 pdb=" CG ASP F 9 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASP F 9 " 0.025 2.00e-02 2.50e+03 pdb=" OD2 ASP F 9 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 134 " 0.017 2.00e-02 2.50e+03 1.93e-02 9.33e+00 pdb=" CG TRP A 134 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 134 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 134 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 134 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 134 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 134 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 134 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 134 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 134 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 37 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C ALA F 37 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA F 37 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG F 38 " 0.012 2.00e-02 2.50e+03 ... (remaining 1238 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.06: 3987 3.06 - 3.52: 7133 3.52 - 3.98: 10663 3.98 - 4.44: 12490 4.44 - 4.90: 18412 Nonbonded interactions: 52685 Sorted by model distance: nonbonded pdb=" N GLU A 131 " pdb=" N CYS A 132 " model vdw 2.595 2.560 nonbonded pdb=" N THR A 128 " pdb=" OG1 THR A 128 " model vdw 2.604 2.496 nonbonded pdb=" C SER E 67 " pdb=" OG SER E 67 " model vdw 2.613 2.616 nonbonded pdb=" C SER D 67 " pdb=" OG SER D 67 " model vdw 2.615 2.616 nonbonded pdb=" C SER D 54 " pdb=" OG SER D 54 " model vdw 2.620 2.616 ... (remaining 52680 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 'A' and (resid 55 through 277 or resid 286 through 349)) selection = (chain 'B' and (resid 55 through 130 or (resid 131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 132 through 349)) } ncs_group { reference = (chain 'C' and resid 8 through 69) selection = (chain 'D' and (resid 8 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 69)) selection = (chain 'E' and (resid 8 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 69)) selection = (chain 'F' and (resid 8 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 69)) } 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: 0.490 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.620 Find NCS groups from input model: 0.070 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 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 : 0.005 0.076 6935 Z= 0.247 Angle : 0.800 9.888 9357 Z= 0.459 Chirality : 0.047 0.250 995 Planarity : 0.007 0.071 1241 Dihedral : 16.096 86.731 2703 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.54 % Allowed : 11.62 % Favored : 87.84 % 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: -1.23 (0.26), residues: 810 helix: -0.49 (0.21), residues: 455 sheet: -1.21 (0.54), residues: 89 loop : -0.94 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 42 TYR 0.027 0.002 TYR D 63 PHE 0.013 0.001 PHE B 224 TRP 0.051 0.002 TRP A 134 HIS 0.005 0.001 HIS D 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.25 ( 6935) covalent geometry : angle 0.79974 / 0.46 ( 9357) hydrogen bonds : bond 0.10702 / 7.12 ( 379) hydrogen bonds : angle 6.03232 / 4.10 ( 1107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.228 Fit side-chains REVERT: A 235 MET cc_start: 0.7877 (pmm) cc_final: 0.7538 (pmm) REVERT: B 210 MET cc_start: 0.7620 (ppp) cc_final: 0.7230 (ppp) REVERT: C 22 LEU cc_start: 0.9314 (mt) cc_final: 0.8934 (mt) REVERT: C 24 GLN cc_start: 0.8801 (mt0) cc_final: 0.8354 (mt0) REVERT: D 40 ASN cc_start: 0.8450 (m110) cc_final: 0.8098 (m-40) REVERT: D 52 ILE cc_start: 0.9017 (mt) cc_final: 0.8794 (pt) REVERT: F 22 LEU cc_start: 0.9343 (mt) cc_final: 0.9041 (mt) REVERT: E 19 ILE cc_start: 0.9328 (pt) cc_final: 0.8954 (tt) REVERT: E 30 ASN cc_start: 0.8571 (t0) cc_final: 0.8112 (t0) REVERT: E 40 ASN cc_start: 0.8561 (m110) cc_final: 0.8286 (m-40) REVERT: E 45 TRP cc_start: 0.8501 (t60) cc_final: 0.8295 (t60) REVERT: E 52 ILE cc_start: 0.9039 (mt) cc_final: 0.8768 (pt) REVERT: E 60 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7838 (pp) outliers start: 4 outliers final: 0 residues processed: 87 average time/residue: 0.0653 time to fit residues: 7.8047 Evaluate side-chains 87 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4258 r_free = 0.4258 target = 0.119303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.104656 restraints weight = 21272.658| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 4.68 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6935 Z= 0.134 Angle : 0.482 6.093 9357 Z= 0.261 Chirality : 0.037 0.123 995 Planarity : 0.004 0.031 1241 Dihedral : 4.163 29.039 924 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.08 % Allowed : 11.89 % Favored : 87.03 % 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: 0.45 (0.28), residues: 810 helix: 1.17 (0.23), residues: 456 sheet: -1.10 (0.54), residues: 89 loop : -0.58 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.009 0.001 TYR D 63 PHE 0.006 0.001 PHE B 216 TRP 0.013 0.001 TRP A 134 HIS 0.002 0.001 HIS D 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 ( 6935) covalent geometry : angle 0.48155 / 0.26 ( 9357) hydrogen bonds : bond 0.03887 / 2.53 ( 379) hydrogen bonds : angle 4.70490 / 3.28 ( 1107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: C 22 LEU cc_start: 0.9332 (mt) cc_final: 0.8962 (mt) REVERT: C 24 GLN cc_start: 0.8839 (mt0) cc_final: 0.8419 (mt0) REVERT: D 40 ASN cc_start: 0.8493 (m110) cc_final: 0.8071 (m-40) REVERT: D 52 ILE cc_start: 0.9031 (mt) cc_final: 0.8810 (pt) REVERT: F 22 LEU cc_start: 0.9391 (mt) cc_final: 0.9086 (mt) REVERT: E 19 ILE cc_start: 0.9345 (pt) cc_final: 0.9006 (tt) REVERT: E 30 ASN cc_start: 0.8587 (t0) cc_final: 0.8273 (t0) REVERT: E 40 ASN cc_start: 0.8643 (m110) cc_final: 0.8362 (m-40) REVERT: E 60 LEU cc_start: 0.8153 (tt) cc_final: 0.7832 (pp) outliers start: 8 outliers final: 3 residues processed: 86 average time/residue: 0.0735 time to fit residues: 8.7447 Evaluate side-chains 84 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain F residue 32 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 0.0060 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 70 optimal weight: 0.0970 chunk 46 optimal weight: 10.0000 overall best weight: 4.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4182 r_free = 0.4182 target = 0.111912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.095998 restraints weight = 21197.492| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 4.66 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 6935 Z= 0.264 Angle : 0.566 6.117 9357 Z= 0.326 Chirality : 0.039 0.124 995 Planarity : 0.005 0.034 1241 Dihedral : 3.892 18.303 922 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.95 % Allowed : 12.57 % Favored : 86.49 % 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: 0.92 (0.30), residues: 810 helix: 1.51 (0.24), residues: 461 sheet: -0.91 (0.54), residues: 89 loop : -0.35 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 46 TYR 0.011 0.001 TYR F 63 PHE 0.009 0.001 PHE A 301 TRP 0.020 0.002 TRP A 134 HIS 0.002 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.26 ( 6935) covalent geometry : angle 0.56577 / 0.33 ( 9357) hydrogen bonds : bond 0.04268 / 2.75 ( 379) hydrogen bonds : angle 5.19977 / 3.71 ( 1107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.280 Fit side-chains REVERT: A 185 VAL cc_start: 0.8466 (t) cc_final: 0.8205 (p) REVERT: A 253 MET cc_start: 0.8446 (mmp) cc_final: 0.7941 (mmm) REVERT: B 210 MET cc_start: 0.7671 (ppp) cc_final: 0.7203 (ppp) REVERT: B 253 MET cc_start: 0.8609 (mmm) cc_final: 0.8403 (mmm) REVERT: C 22 LEU cc_start: 0.9427 (mt) cc_final: 0.9069 (mt) REVERT: C 24 GLN cc_start: 0.9014 (mt0) cc_final: 0.8575 (mt0) REVERT: D 40 ASN cc_start: 0.8512 (m110) cc_final: 0.8095 (m-40) REVERT: D 52 ILE cc_start: 0.9116 (mt) cc_final: 0.8904 (tt) REVERT: F 22 LEU cc_start: 0.9447 (mt) cc_final: 0.9109 (mt) REVERT: E 19 ILE cc_start: 0.9352 (pt) cc_final: 0.9000 (tt) REVERT: E 30 ASN cc_start: 0.8632 (t0) cc_final: 0.8359 (t0) REVERT: E 40 ASN cc_start: 0.8692 (m110) cc_final: 0.8420 (m-40) REVERT: E 60 LEU cc_start: 0.8218 (tt) cc_final: 0.7916 (pp) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.1004 time to fit residues: 12.1257 Evaluate side-chains 92 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 34 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4253 r_free = 0.4253 target = 0.118572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.103847 restraints weight = 21284.366| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 4.65 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 6935 Z= 0.110 Angle : 0.463 7.692 9357 Z= 0.244 Chirality : 0.037 0.129 995 Planarity : 0.004 0.029 1241 Dihedral : 3.682 18.648 922 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.08 % Allowed : 12.97 % Favored : 85.95 % 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 (0.30), residues: 810 helix: 2.18 (0.24), residues: 448 sheet: -0.73 (0.55), residues: 89 loop : -0.26 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 104 TYR 0.010 0.001 TYR D 63 PHE 0.008 0.001 PHE A 298 TRP 0.022 0.001 TRP A 134 HIS 0.004 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 6935) covalent geometry : angle 0.46346 / 0.24 ( 9357) hydrogen bonds : bond 0.03724 / 2.41 ( 379) hydrogen bonds : angle 4.41339 / 3.12 ( 1107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.289 Fit side-chains REVERT: A 253 MET cc_start: 0.8227 (mmp) cc_final: 0.7871 (mmm) REVERT: B 210 MET cc_start: 0.7617 (ppp) cc_final: 0.7295 (ppp) REVERT: C 22 LEU cc_start: 0.9358 (mt) cc_final: 0.8980 (mt) REVERT: C 24 GLN cc_start: 0.8923 (mt0) cc_final: 0.8485 (mt0) REVERT: D 40 ASN cc_start: 0.8386 (m110) cc_final: 0.7956 (m-40) REVERT: D 52 ILE cc_start: 0.9086 (mt) cc_final: 0.8846 (tt) REVERT: F 22 LEU cc_start: 0.9409 (mt) cc_final: 0.9069 (mt) REVERT: F 32 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: E 12 LEU cc_start: 0.7620 (tt) cc_final: 0.7397 (mt) REVERT: E 19 ILE cc_start: 0.9359 (pt) cc_final: 0.9016 (tt) REVERT: E 30 ASN cc_start: 0.8575 (t0) cc_final: 0.8287 (t0) REVERT: E 40 ASN cc_start: 0.8642 (m110) cc_final: 0.8354 (m-40) outliers start: 8 outliers final: 1 residues processed: 92 average time/residue: 0.0965 time to fit residues: 11.6326 Evaluate side-chains 87 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain F residue 32 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 74 optimal weight: 0.2980 chunk 31 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 69 optimal weight: 9.9990 overall best weight: 3.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4198 r_free = 0.4198 target = 0.112887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.096891 restraints weight = 21072.946| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 4.80 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6935 Z= 0.199 Angle : 0.526 9.987 9357 Z= 0.288 Chirality : 0.038 0.124 995 Planarity : 0.004 0.031 1241 Dihedral : 3.652 17.929 922 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.22 % Allowed : 13.65 % Favored : 85.14 % 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: 1.53 (0.30), residues: 810 helix: 2.11 (0.25), residues: 448 sheet: -0.73 (0.54), residues: 89 loop : -0.15 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 104 TYR 0.010 0.001 TYR D 63 PHE 0.007 0.001 PHE A 301 TRP 0.025 0.001 TRP A 134 HIS 0.005 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.20 ( 6935) covalent geometry : angle 0.52617 / 0.29 ( 9357) hydrogen bonds : bond 0.03852 / 2.49 ( 379) hydrogen bonds : angle 4.80615 / 3.42 ( 1107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.285 Fit side-chains REVERT: A 104 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.7971 (mtp-110) REVERT: A 253 MET cc_start: 0.8458 (mmp) cc_final: 0.7967 (mmm) REVERT: B 210 MET cc_start: 0.7641 (ppp) cc_final: 0.7397 (ppp) REVERT: C 22 LEU cc_start: 0.9405 (mt) cc_final: 0.9054 (mt) REVERT: C 24 GLN cc_start: 0.8986 (mt0) cc_final: 0.8541 (mt0) REVERT: C 32 GLU cc_start: 0.7613 (mp0) cc_final: 0.7281 (mp0) REVERT: D 40 ASN cc_start: 0.8466 (m110) cc_final: 0.8051 (m-40) REVERT: D 52 ILE cc_start: 0.9117 (mt) cc_final: 0.8893 (tt) REVERT: F 22 LEU cc_start: 0.9437 (mt) cc_final: 0.9094 (mt) REVERT: E 12 LEU cc_start: 0.7758 (tt) cc_final: 0.7549 (mt) REVERT: E 19 ILE cc_start: 0.9346 (pt) cc_final: 0.9020 (tt) REVERT: E 30 ASN cc_start: 0.8618 (t0) cc_final: 0.8331 (t0) REVERT: E 40 ASN cc_start: 0.8686 (m110) cc_final: 0.8426 (m-40) REVERT: E 60 LEU cc_start: 0.8239 (tt) cc_final: 0.7879 (pp) outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 0.1135 time to fit residues: 13.5465 Evaluate side-chains 90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 34 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 34 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4192 r_free = 0.4192 target = 0.112647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.096606 restraints weight = 21375.287| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 4.78 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6935 Z= 0.208 Angle : 0.530 8.602 9357 Z= 0.293 Chirality : 0.039 0.123 995 Planarity : 0.004 0.062 1241 Dihedral : 3.683 17.749 922 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.95 % Allowed : 15.14 % Favored : 83.92 % 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: 1.40 (0.30), residues: 810 helix: 1.91 (0.24), residues: 453 sheet: -0.77 (0.53), residues: 89 loop : -0.08 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 104 TYR 0.007 0.001 TYR F 63 PHE 0.007 0.001 PHE A 301 TRP 0.028 0.001 TRP A 134 HIS 0.004 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.21 ( 6935) covalent geometry : angle 0.52976 / 0.29 ( 9357) hydrogen bonds : bond 0.03961 / 2.56 ( 379) hydrogen bonds : angle 4.91025 / 3.50 ( 1107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.308 Fit side-chains REVERT: A 253 MET cc_start: 0.8499 (mmp) cc_final: 0.7996 (mmm) REVERT: B 210 MET cc_start: 0.7638 (ppp) cc_final: 0.7356 (ppp) REVERT: C 22 LEU cc_start: 0.9414 (mt) cc_final: 0.9056 (mt) REVERT: C 24 GLN cc_start: 0.9004 (mt0) cc_final: 0.8599 (mt0) REVERT: D 40 ASN cc_start: 0.8471 (m110) cc_final: 0.8123 (m-40) REVERT: D 52 ILE cc_start: 0.9140 (mt) cc_final: 0.8893 (tt) REVERT: F 22 LEU cc_start: 0.9437 (mt) cc_final: 0.9136 (mt) REVERT: E 19 ILE cc_start: 0.9348 (pt) cc_final: 0.9013 (tt) REVERT: E 30 ASN cc_start: 0.8620 (t0) cc_final: 0.8342 (t0) REVERT: E 40 ASN cc_start: 0.8682 (m110) cc_final: 0.8427 (m-40) REVERT: E 60 LEU cc_start: 0.8313 (tt) cc_final: 0.7847 (pp) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.1121 time to fit residues: 13.2332 Evaluate side-chains 91 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 49 optimal weight: 0.0170 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4214 r_free = 0.4214 target = 0.114036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.098296 restraints weight = 20997.225| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 4.73 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6935 Z= 0.148 Angle : 0.499 7.963 9357 Z= 0.268 Chirality : 0.038 0.125 995 Planarity : 0.004 0.048 1241 Dihedral : 3.628 17.888 922 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.35 % Allowed : 15.27 % Favored : 83.38 % 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: 1.65 (0.31), residues: 810 helix: 2.16 (0.25), residues: 448 sheet: -0.81 (0.52), residues: 89 loop : 0.03 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 104 TYR 0.008 0.001 TYR D 63 PHE 0.009 0.001 PHE A 118 TRP 0.030 0.001 TRP A 134 HIS 0.003 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 ( 6935) covalent geometry : angle 0.49864 / 0.27 ( 9357) hydrogen bonds : bond 0.03780 / 2.45 ( 379) hydrogen bonds : angle 4.58683 / 3.26 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.301 Fit side-chains REVERT: A 104 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7942 (mtp-110) REVERT: A 253 MET cc_start: 0.8508 (mmp) cc_final: 0.8027 (mmm) REVERT: A 337 ARG cc_start: 0.8815 (ptp-170) cc_final: 0.8486 (mtt180) REVERT: B 210 MET cc_start: 0.7648 (ppp) cc_final: 0.7176 (ppp) REVERT: B 235 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7578 (pmm) REVERT: B 253 MET cc_start: 0.8504 (mmm) cc_final: 0.8232 (mmm) REVERT: C 22 LEU cc_start: 0.9397 (mt) cc_final: 0.9035 (mt) REVERT: C 24 GLN cc_start: 0.8999 (mt0) cc_final: 0.8587 (mt0) REVERT: D 40 ASN cc_start: 0.8441 (m110) cc_final: 0.8095 (m-40) REVERT: D 52 ILE cc_start: 0.9120 (mt) cc_final: 0.8858 (tt) REVERT: F 22 LEU cc_start: 0.9425 (mt) cc_final: 0.9080 (mt) REVERT: E 12 LEU cc_start: 0.7695 (tt) cc_final: 0.7453 (mt) REVERT: E 30 ASN cc_start: 0.8608 (t0) cc_final: 0.8324 (t0) REVERT: E 40 ASN cc_start: 0.8663 (m110) cc_final: 0.8406 (m-40) REVERT: E 60 LEU cc_start: 0.8276 (tt) cc_final: 0.7817 (pp) outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.1134 time to fit residues: 13.1617 Evaluate side-chains 90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain E residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.0770 chunk 66 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4251 r_free = 0.4251 target = 0.116267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.101073 restraints weight = 21311.781| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 4.67 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 6935 Z= 0.098 Angle : 0.473 7.346 9357 Z= 0.245 Chirality : 0.037 0.126 995 Planarity : 0.004 0.040 1241 Dihedral : 3.550 18.044 922 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.68 % Allowed : 16.08 % Favored : 83.24 % 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: 1.91 (0.31), residues: 810 helix: 2.42 (0.25), residues: 448 sheet: -0.74 (0.52), residues: 89 loop : 0.07 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 104 TYR 0.008 0.001 TYR D 63 PHE 0.008 0.001 PHE A 118 TRP 0.034 0.001 TRP A 134 HIS 0.002 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 ( 6935) covalent geometry : angle 0.47253 / 0.24 ( 9357) hydrogen bonds : bond 0.03440 / 2.25 ( 379) hydrogen bonds : angle 4.15202 / 2.93 ( 1107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.297 Fit side-chains REVERT: A 253 MET cc_start: 0.8474 (mmp) cc_final: 0.8049 (mmm) REVERT: B 210 MET cc_start: 0.7628 (ppp) cc_final: 0.7002 (ppp) REVERT: B 235 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7510 (pmm) REVERT: B 253 MET cc_start: 0.8482 (mmm) cc_final: 0.8218 (mmm) REVERT: C 22 LEU cc_start: 0.9378 (mt) cc_final: 0.9022 (mt) REVERT: C 24 GLN cc_start: 0.8966 (mt0) cc_final: 0.8534 (mt0) REVERT: D 40 ASN cc_start: 0.8416 (m110) cc_final: 0.8075 (m-40) REVERT: D 52 ILE cc_start: 0.9069 (mt) cc_final: 0.8821 (tt) REVERT: F 22 LEU cc_start: 0.9400 (mt) cc_final: 0.9082 (mt) REVERT: E 30 ASN cc_start: 0.8613 (t0) cc_final: 0.8308 (t0) REVERT: E 40 ASN cc_start: 0.8595 (m110) cc_final: 0.8336 (m-40) REVERT: E 60 LEU cc_start: 0.8215 (tt) cc_final: 0.7791 (pp) outliers start: 5 outliers final: 1 residues processed: 84 average time/residue: 0.1128 time to fit residues: 12.2246 Evaluate side-chains 82 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain B residue 235 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 0.3980 chunk 53 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4204 r_free = 0.4204 target = 0.115974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.100746 restraints weight = 21239.494| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 4.70 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6935 Z= 0.237 Angle : 0.551 7.080 9357 Z= 0.312 Chirality : 0.039 0.128 995 Planarity : 0.004 0.037 1241 Dihedral : 3.560 17.603 922 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.95 % Allowed : 15.41 % Favored : 83.65 % 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 (0.31), residues: 810 helix: 2.07 (0.25), residues: 453 sheet: -0.76 (0.52), residues: 89 loop : 0.06 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 104 TYR 0.009 0.001 TYR F 63 PHE 0.006 0.001 PHE A 301 TRP 0.032 0.002 TRP A 134 HIS 0.003 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.24 ( 6935) covalent geometry : angle 0.55061 / 0.31 ( 9357) hydrogen bonds : bond 0.03905 / 2.52 ( 379) hydrogen bonds : angle 4.85298 / 3.46 ( 1107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.273 Fit side-chains REVERT: A 185 VAL cc_start: 0.8629 (t) cc_final: 0.8406 (p) REVERT: A 253 MET cc_start: 0.8446 (mmp) cc_final: 0.8034 (mmm) REVERT: B 210 MET cc_start: 0.7604 (ppp) cc_final: 0.7096 (ppp) REVERT: B 235 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7637 (pmm) REVERT: C 20 LYS cc_start: 0.8796 (tttt) cc_final: 0.8591 (ttmt) REVERT: C 22 LEU cc_start: 0.9425 (mt) cc_final: 0.9075 (mt) REVERT: C 24 GLN cc_start: 0.8972 (mt0) cc_final: 0.8558 (mt0) REVERT: D 40 ASN cc_start: 0.8505 (m110) cc_final: 0.8091 (m-40) REVERT: D 52 ILE cc_start: 0.9152 (mt) cc_final: 0.8902 (tt) REVERT: F 22 LEU cc_start: 0.9436 (mt) cc_final: 0.9107 (mt) REVERT: E 12 LEU cc_start: 0.7765 (tt) cc_final: 0.7558 (mt) REVERT: E 30 ASN cc_start: 0.8616 (t0) cc_final: 0.8300 (t0) REVERT: E 40 ASN cc_start: 0.8706 (m110) cc_final: 0.8456 (m-40) REVERT: E 60 LEU cc_start: 0.8259 (tt) cc_final: 0.7891 (pp) outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.1108 time to fit residues: 12.9971 Evaluate side-chains 93 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain F residue 10 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 0.2980 chunk 39 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4259 r_free = 0.4259 target = 0.119039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.104620 restraints weight = 21168.100| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 4.74 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 6935 Z= 0.102 Angle : 0.487 7.144 9357 Z= 0.255 Chirality : 0.037 0.126 995 Planarity : 0.004 0.036 1241 Dihedral : 3.569 17.868 922 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.54 % Allowed : 16.22 % Favored : 83.24 % 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: 1.88 (0.31), residues: 810 helix: 2.37 (0.25), residues: 448 sheet: -0.68 (0.53), residues: 89 loop : 0.09 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 104 TYR 0.009 0.001 TYR D 63 PHE 0.009 0.001 PHE A 118 TRP 0.035 0.001 TRP A 134 HIS 0.002 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 6935) covalent geometry : angle 0.48691 / 0.25 ( 9357) hydrogen bonds : bond 0.03508 / 2.28 ( 379) hydrogen bonds : angle 4.20529 / 2.95 ( 1107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.7464 (ptm160) cc_final: 0.7141 (ptm160) REVERT: A 253 MET cc_start: 0.8391 (mmp) cc_final: 0.8073 (mmm) REVERT: B 210 MET cc_start: 0.7637 (ppp) cc_final: 0.7131 (ppp) REVERT: B 235 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7428 (pmm) REVERT: B 266 LYS cc_start: 0.8013 (mptt) cc_final: 0.6892 (tppt) REVERT: C 20 LYS cc_start: 0.8718 (tttt) cc_final: 0.8510 (ttmt) REVERT: C 22 LEU cc_start: 0.9391 (mt) cc_final: 0.9034 (mt) REVERT: C 24 GLN cc_start: 0.8991 (mt0) cc_final: 0.8587 (mt0) REVERT: D 40 ASN cc_start: 0.8497 (m110) cc_final: 0.8163 (m-40) REVERT: D 52 ILE cc_start: 0.9113 (mt) cc_final: 0.8855 (tt) REVERT: F 22 LEU cc_start: 0.9404 (mt) cc_final: 0.9086 (mt) REVERT: E 12 LEU cc_start: 0.7579 (tt) cc_final: 0.7363 (mt) REVERT: E 30 ASN cc_start: 0.8564 (t0) cc_final: 0.8256 (t0) REVERT: E 40 ASN cc_start: 0.8663 (m110) cc_final: 0.8409 (m-40) REVERT: E 60 LEU cc_start: 0.8209 (tt) cc_final: 0.7771 (pp) outliers start: 4 outliers final: 3 residues processed: 81 average time/residue: 0.1138 time to fit residues: 11.7131 Evaluate side-chains 83 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain F residue 10 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 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 = 0.4201 r_free = 0.4201 target = 0.113149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.097313 restraints weight = 20866.358| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 4.74 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6935 Z= 0.195 Angle : 0.525 6.829 9357 Z= 0.291 Chirality : 0.039 0.126 995 Planarity : 0.004 0.035 1241 Dihedral : 3.503 17.769 922 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.81 % Allowed : 16.08 % Favored : 83.11 % 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: 1.75 (0.31), residues: 810 helix: 2.21 (0.25), residues: 448 sheet: -0.67 (0.53), residues: 89 loop : 0.11 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 104 TYR 0.010 0.001 TYR D 63 PHE 0.006 0.001 PHE A 301 TRP 0.033 0.001 TRP A 134 HIS 0.002 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.19 ( 6935) covalent geometry : angle 0.52518 / 0.29 ( 9357) hydrogen bonds : bond 0.03741 / 2.42 ( 379) hydrogen bonds : angle 4.64542 / 3.30 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1484.97 seconds wall clock time: 26 minutes 11.66 seconds (1571.66 seconds total)