Starting phenix.real_space_refine on Fri Sep 11 04:50:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ck6_30382/09_2026/7ck6_30382.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ck6_30382/09_2026/7ck6_30382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ck6_30382/09_2026/7ck6_30382.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ck6_30382/09_2026/7ck6_30382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ck6_30382/09_2026/7ck6_30382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ck6_30382/09_2026/7ck6_30382.map" model { file = "/net/cci-nas-00/data/ceres_data/7ck6_30382/09_2026/7ck6_30382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ck6_30382/09_2026/7ck6_30382.cif" } resolution = 3.4 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= 0.000 sd= 0.002 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 1 5.49 5 S 32 5.16 5 C 4808 2.51 5 N 1281 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7460 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "B" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "E" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "F" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "G" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "H" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "I" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "J" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.42, per 1000 atoms: 0.19 Number of scatterers: 7460 At special positions: 0 Unit cell: (111.24, 145.8, 96.12, 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 32 16.00 P 1 15.00 O 1338 8.00 N 1281 7.00 C 4808 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: 0.51 Conformation dependent library (CDL) restraints added in 350.6 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 37.0% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'C' and resid 67 through 118 Proline residue: C 98 - end of helix removed outlier: 3.784A pdb=" N GLU C 102 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 96 Processing helix chain 'D' and resid 96 through 118 Processing helix chain 'E' and resid 24 through 35 Processing helix chain 'E' and resid 42 through 66 removed outlier: 3.509A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 35 Processing helix chain 'F' and resid 43 through 66 Processing helix chain 'G' and resid 7 through 37 removed outlier: 3.892A pdb=" N TRP G 25 " --> pdb=" O PHE G 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 48 through 54 removed outlier: 3.567A pdb=" N LEU G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 37 removed outlier: 3.893A pdb=" N TRP H 25 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Proline residue: H 29 - end of helix removed outlier: 3.505A pdb=" N LYS H 37 " --> pdb=" O TYR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 removed outlier: 3.567A pdb=" N LEU H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 48 Proline residue: I 42 - end of helix removed outlier: 3.793A pdb=" N LYS I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 48 " --> pdb=" O ILE I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 48 Proline residue: J 42 - end of helix removed outlier: 3.793A pdb=" N LYS J 47 " --> pdb=" O PHE J 43 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU J 48 " --> pdb=" O ILE J 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 353 removed outlier: 3.731A pdb=" N LYS A 351 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 14.431A pdb=" N VAL A 186 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N ASP A 209 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TRP A 188 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER A 214 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 301 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 337 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 351 through 353 removed outlier: 3.669A pdb=" N LYS B 351 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 14.430A pdb=" N VAL B 186 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ASP B 209 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TRP B 188 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER B 214 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 301 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 337 " --> pdb=" O LEU B 332 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2343 1.33 - 1.45: 1063 1.45 - 1.57: 4157 1.57 - 1.69: 2 1.69 - 1.80: 56 Bond restraints: 7621 Sorted by residual: bond pdb=" C31 PC1 A 401 " pdb=" O31 PC1 A 401 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C21 PC1 A 401 " pdb=" O21 PC1 A 401 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CA HIS A 347 " pdb=" C HIS A 347 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.33e+01 bond pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.32e+01 ... (remaining 7616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 9909 2.67 - 5.35: 329 5.35 - 8.02: 45 8.02 - 10.69: 12 10.69 - 13.36: 4 Bond angle restraints: 10299 Sorted by residual: angle pdb=" N PRO A 333 " pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 110.70 124.06 -13.36 1.22e+00 6.72e-01 1.20e+02 angle pdb=" N PRO B 333 " pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 110.70 124.05 -13.35 1.22e+00 6.72e-01 1.20e+02 angle pdb=" C GLU H 46 " pdb=" N PRO H 47 " pdb=" CA PRO H 47 " ideal model delta sigma weight residual 119.84 132.57 -12.73 1.25e+00 6.40e-01 1.04e+02 angle pdb=" C GLU G 46 " pdb=" N PRO G 47 " pdb=" CA PRO G 47 " ideal model delta sigma weight residual 119.84 132.41 -12.57 1.25e+00 6.40e-01 1.01e+02 angle pdb=" N THR B 292 " pdb=" CA THR B 292 " pdb=" C THR B 292 " ideal model delta sigma weight residual 111.14 119.93 -8.79 1.08e+00 8.57e-01 6.62e+01 ... (remaining 10294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 3942 15.13 - 30.26: 468 30.26 - 45.39: 82 45.39 - 60.51: 24 60.51 - 75.64: 7 Dihedral angle restraints: 4523 sinusoidal: 1855 harmonic: 2668 Sorted by residual: dihedral pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual 122.80 134.15 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CA GLN A 182 " pdb=" CB GLN A 182 " ideal model delta harmonic sigma weight residual 122.80 134.05 -11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" C GLN B 182 " pdb=" N GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual -122.60 -133.46 10.86 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 4520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1029 0.096 - 0.192: 96 0.192 - 0.288: 13 0.288 - 0.384: 3 0.384 - 0.480: 2 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA GLN B 182 " pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CB GLN B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CA GLN A 182 " pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CB GLN A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" C PRO A 333 " pdb=" CB PRO A 333 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1140 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 46 " -0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO H 47 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO H 47 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 47 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 46 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO G 47 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 47 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 47 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 66 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C THR C 66 " 0.044 2.00e-02 2.50e+03 pdb=" O THR C 66 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE C 67 " -0.015 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 29 2.30 - 2.95: 3720 2.95 - 3.60: 10402 3.60 - 4.25: 14230 4.25 - 4.90: 25368 Nonbonded interactions: 53749 Sorted by model distance: nonbonded pdb=" O ASN F 39 " pdb=" CE2 PHE F 41 " model vdw 1.652 3.340 nonbonded pdb=" O LEU H 30 " pdb=" CD2 LEU H 34 " model vdw 1.677 3.460 nonbonded pdb=" O ASP F 37 " pdb=" OD1 ASP F 40 " model vdw 1.722 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" ND2 ASN F 48 " model vdw 1.824 3.120 nonbonded pdb=" O LEU G 30 " pdb=" CD2 LEU G 34 " model vdw 1.843 3.460 ... (remaining 53744 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 77 through 360) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.970 Find NCS groups from input model: 0.110 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 : 0.008 0.125 7621 Z= 0.400 Angle : 1.142 13.363 10299 Z= 0.740 Chirality : 0.065 0.480 1143 Planarity : 0.005 0.065 1310 Dihedral : 13.479 75.643 2807 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 36.32 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.11 % Favored : 93.12 % Rotamer: Outliers : 4.12 % Allowed : 12.38 % Favored : 83.50 % Cbeta Deviations : 0.23 % 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: 0.38 (0.28), residues: 916 helix: 2.24 (0.30), residues: 300 sheet: 0.39 (0.27), residues: 378 loop : -2.66 (0.34), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 21 TYR 0.018 0.002 TYR A 129 PHE 0.031 0.002 PHE A 344 TRP 0.009 0.001 TRP C 86 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.40 ( 7621) covalent geometry : angle 1.14224 / 0.74 (10299) hydrogen bonds : bond 0.16553 / 11.14 ( 518) hydrogen bonds : angle 6.11566 / 4.22 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 ASP cc_start: 0.7206 (m-30) cc_final: 0.6707 (m-30) REVERT: C 97 LEU cc_start: 0.8892 (tp) cc_final: 0.8644 (tp) REVERT: C 114 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9087 (mt) REVERT: I 38 LEU cc_start: 0.9032 (mm) cc_final: 0.8766 (mm) outliers start: 33 outliers final: 12 residues processed: 319 average time/residue: 0.1191 time to fit residues: 46.6712 Evaluate side-chains 174 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN A 114 GLN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 220 HIS A 223 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN B 97 GLN B 114 GLN B 163 GLN B 182 GLN B 220 HIS B 223 GLN ** B 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN C 110 GLN E 23 ASN E 61 ASN F 61 ASN G 10 GLN H 10 GLN H 13 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.070381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.053116 restraints weight = 31494.539| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.88 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7621 Z= 0.275 Angle : 0.920 9.457 10299 Z= 0.471 Chirality : 0.049 0.228 1143 Planarity : 0.006 0.053 1310 Dihedral : 8.029 57.926 1061 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.24 % Favored : 94.32 % Rotamer: Outliers : 6.00 % Allowed : 21.50 % Favored : 72.50 % 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: 0.96 (0.28), residues: 916 helix: 2.49 (0.28), residues: 308 sheet: 1.01 (0.26), residues: 372 loop : -2.69 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 18 TYR 0.019 0.002 TYR A 129 PHE 0.039 0.003 PHE E 34 TRP 0.018 0.002 TRP G 54 HIS 0.007 0.002 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.28 ( 7621) covalent geometry : angle 0.92026 / 0.47 (10299) hydrogen bonds : bond 0.05258 / 3.62 ( 518) hydrogen bonds : angle 5.37548 / 3.71 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7421 (t0) REVERT: A 150 LEU cc_start: 0.9268 (mp) cc_final: 0.8607 (tt) REVERT: A 154 MET cc_start: 0.8609 (ttt) cc_final: 0.8181 (tpt) REVERT: A 270 MET cc_start: 0.8413 (mpp) cc_final: 0.8168 (mpp) REVERT: B 128 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7120 (t0) REVERT: B 154 MET cc_start: 0.8527 (ttt) cc_final: 0.8120 (tpt) REVERT: B 160 LEU cc_start: 0.9338 (tt) cc_final: 0.8962 (tt) REVERT: B 270 MET cc_start: 0.8412 (mpp) cc_final: 0.8142 (mpp) REVERT: B 280 ASP cc_start: 0.8958 (p0) cc_final: 0.8690 (p0) REVERT: B 293 ARG cc_start: 0.8368 (mmm160) cc_final: 0.7993 (mmm160) REVERT: C 97 LEU cc_start: 0.9417 (tp) cc_final: 0.9057 (tp) REVERT: C 101 PHE cc_start: 0.9351 (m-80) cc_final: 0.9034 (m-80) REVERT: C 108 MET cc_start: 0.9530 (mmp) cc_final: 0.9111 (mmp) REVERT: I 17 LYS cc_start: 0.9682 (mttt) cc_final: 0.9364 (mtmt) REVERT: I 32 LEU cc_start: 0.9741 (mt) cc_final: 0.9523 (pp) REVERT: I 38 LEU cc_start: 0.9260 (mm) cc_final: 0.8923 (mm) REVERT: J 17 LYS cc_start: 0.9594 (mttt) cc_final: 0.9219 (mtmt) outliers start: 48 outliers final: 22 residues processed: 201 average time/residue: 0.0809 time to fit residues: 22.3209 Evaluate side-chains 180 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain I residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN F 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.069268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.051389 restraints weight = 32398.080| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 5.11 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7621 Z= 0.215 Angle : 0.854 11.948 10299 Z= 0.425 Chirality : 0.049 0.250 1143 Planarity : 0.005 0.049 1310 Dihedral : 7.571 58.415 1046 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.42 % Favored : 92.36 % Rotamer: Outliers : 5.50 % Allowed : 24.38 % Favored : 70.12 % 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: 1.21 (0.28), residues: 916 helix: 2.59 (0.28), residues: 310 sheet: 1.21 (0.26), residues: 370 loop : -2.51 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 173 TYR 0.031 0.002 TYR J 34 PHE 0.021 0.002 PHE E 34 TRP 0.010 0.002 TRP G 54 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 ( 7621) covalent geometry : angle 0.85399 / 0.42 (10299) hydrogen bonds : bond 0.04803 / 3.31 ( 518) hydrogen bonds : angle 5.18332 / 3.56 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7534 (t0) REVERT: A 154 MET cc_start: 0.8624 (ttt) cc_final: 0.8254 (tpt) REVERT: A 270 MET cc_start: 0.8303 (mpp) cc_final: 0.8022 (mpp) REVERT: B 154 MET cc_start: 0.8562 (ttt) cc_final: 0.8181 (tpt) REVERT: B 160 LEU cc_start: 0.9323 (tt) cc_final: 0.8928 (tt) REVERT: B 270 MET cc_start: 0.8313 (mpp) cc_final: 0.8005 (mpp) REVERT: C 97 LEU cc_start: 0.9392 (tp) cc_final: 0.8889 (tp) REVERT: C 101 PHE cc_start: 0.9357 (m-80) cc_final: 0.8951 (m-80) REVERT: C 108 MET cc_start: 0.9526 (mmp) cc_final: 0.9209 (mmp) REVERT: I 38 LEU cc_start: 0.9236 (mm) cc_final: 0.8900 (mm) outliers start: 44 outliers final: 22 residues processed: 193 average time/residue: 0.0811 time to fit residues: 21.5158 Evaluate side-chains 176 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 35 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN H 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.069080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.051584 restraints weight = 32868.703| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 5.07 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7621 Z= 0.201 Angle : 0.852 13.931 10299 Z= 0.412 Chirality : 0.049 0.287 1143 Planarity : 0.005 0.050 1310 Dihedral : 7.641 59.324 1046 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.77 % Favored : 93.01 % Rotamer: Outliers : 5.00 % Allowed : 25.50 % Favored : 69.50 % 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 (0.29), residues: 916 helix: 2.57 (0.29), residues: 310 sheet: 1.09 (0.26), residues: 372 loop : -2.23 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 293 TYR 0.017 0.002 TYR B 129 PHE 0.016 0.002 PHE E 34 TRP 0.008 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 7621) covalent geometry : angle 0.85222 / 0.41 (10299) hydrogen bonds : bond 0.04551 / 3.14 ( 518) hydrogen bonds : angle 5.07601 / 3.49 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.9167 (p0) cc_final: 0.8907 (m-40) REVERT: A 128 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7569 (t0) REVERT: A 154 MET cc_start: 0.8596 (ttt) cc_final: 0.8260 (tpt) REVERT: A 280 ASP cc_start: 0.8942 (p0) cc_final: 0.8640 (p0) REVERT: B 116 ASN cc_start: 0.9135 (p0) cc_final: 0.8881 (m-40) REVERT: B 198 ASP cc_start: 0.9229 (p0) cc_final: 0.8934 (t0) REVERT: B 280 ASP cc_start: 0.8955 (p0) cc_final: 0.8692 (p0) REVERT: B 296 ASP cc_start: 0.9013 (t0) cc_final: 0.8776 (t0) REVERT: C 97 LEU cc_start: 0.9336 (tp) cc_final: 0.8817 (tp) REVERT: C 101 PHE cc_start: 0.9352 (m-80) cc_final: 0.8954 (m-80) REVERT: C 108 MET cc_start: 0.9554 (mmp) cc_final: 0.9191 (mmp) REVERT: I 34 TYR cc_start: 0.9132 (t80) cc_final: 0.8927 (t80) REVERT: I 38 LEU cc_start: 0.9239 (mm) cc_final: 0.8899 (mm) outliers start: 40 outliers final: 27 residues processed: 185 average time/residue: 0.0782 time to fit residues: 20.2120 Evaluate side-chains 180 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 0.0010 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 113 GLN G 13 GLN H 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.067532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.050059 restraints weight = 33096.112| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 5.10 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7621 Z= 0.238 Angle : 0.856 11.902 10299 Z= 0.416 Chirality : 0.049 0.327 1143 Planarity : 0.005 0.061 1310 Dihedral : 7.707 56.803 1046 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 6.00 % Allowed : 26.50 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.29), residues: 916 helix: 2.40 (0.29), residues: 310 sheet: 0.93 (0.26), residues: 376 loop : -2.32 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 173 TYR 0.018 0.002 TYR B 129 PHE 0.019 0.002 PHE C 92 TRP 0.008 0.002 TRP E 57 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 ( 7621) covalent geometry : angle 0.85577 / 0.42 (10299) hydrogen bonds : bond 0.04686 / 3.26 ( 518) hydrogen bonds : angle 5.14426 / 3.53 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8545 (ttm170) cc_final: 0.8229 (ttm110) REVERT: A 116 ASN cc_start: 0.9202 (p0) cc_final: 0.8914 (m-40) REVERT: A 128 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7590 (t0) REVERT: A 280 ASP cc_start: 0.9035 (p0) cc_final: 0.8739 (p0) REVERT: B 88 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8215 (ttm110) REVERT: B 116 ASN cc_start: 0.9193 (p0) cc_final: 0.8953 (m-40) REVERT: B 198 ASP cc_start: 0.9326 (p0) cc_final: 0.8959 (t0) REVERT: B 280 ASP cc_start: 0.9025 (p0) cc_final: 0.8717 (p0) REVERT: C 97 LEU cc_start: 0.9358 (tp) cc_final: 0.8783 (tp) REVERT: C 101 PHE cc_start: 0.9374 (m-80) cc_final: 0.8957 (m-80) REVERT: C 108 MET cc_start: 0.9482 (mmp) cc_final: 0.9218 (mmp) REVERT: C 113 GLN cc_start: 0.9440 (mm110) cc_final: 0.9191 (mm-40) REVERT: I 34 TYR cc_start: 0.9249 (t80) cc_final: 0.8783 (t80) REVERT: I 38 LEU cc_start: 0.9239 (mm) cc_final: 0.8896 (mm) REVERT: J 29 ARG cc_start: 0.9439 (mtm180) cc_final: 0.8916 (mpp80) outliers start: 48 outliers final: 31 residues processed: 191 average time/residue: 0.0773 time to fit residues: 20.6589 Evaluate side-chains 183 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.067358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.050121 restraints weight = 32989.930| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.98 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7621 Z= 0.216 Angle : 0.870 12.845 10299 Z= 0.413 Chirality : 0.049 0.362 1143 Planarity : 0.005 0.055 1310 Dihedral : 7.703 58.869 1043 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 5.25 % Allowed : 28.25 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.29), residues: 916 helix: 2.42 (0.28), residues: 310 sheet: 0.96 (0.26), residues: 374 loop : -2.37 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 117 TYR 0.020 0.002 TYR J 34 PHE 0.020 0.002 PHE C 92 TRP 0.008 0.001 TRP E 57 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 ( 7621) covalent geometry : angle 0.86991 / 0.41 (10299) hydrogen bonds : bond 0.04542 / 3.14 ( 518) hydrogen bonds : angle 5.03873 / 3.46 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8553 (ttm170) cc_final: 0.8202 (ttm110) REVERT: A 116 ASN cc_start: 0.9222 (p0) cc_final: 0.8972 (m-40) REVERT: A 128 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7550 (t0) REVERT: A 280 ASP cc_start: 0.9028 (p0) cc_final: 0.8702 (p0) REVERT: B 88 ARG cc_start: 0.8535 (ttm170) cc_final: 0.8185 (ttm110) REVERT: B 116 ASN cc_start: 0.9216 (p0) cc_final: 0.8952 (m-40) REVERT: B 198 ASP cc_start: 0.9308 (p0) cc_final: 0.8953 (t0) REVERT: B 280 ASP cc_start: 0.9033 (p0) cc_final: 0.8702 (p0) REVERT: B 296 ASP cc_start: 0.8940 (t0) cc_final: 0.8663 (t0) REVERT: C 97 LEU cc_start: 0.9354 (tp) cc_final: 0.8728 (tp) REVERT: C 101 PHE cc_start: 0.9358 (m-80) cc_final: 0.8964 (m-80) REVERT: C 108 MET cc_start: 0.9467 (mmp) cc_final: 0.9160 (mmp) REVERT: I 34 TYR cc_start: 0.9183 (t80) cc_final: 0.8946 (t80) REVERT: I 38 LEU cc_start: 0.9240 (mm) cc_final: 0.8908 (mm) REVERT: J 29 ARG cc_start: 0.9438 (mtm180) cc_final: 0.8875 (mpp80) outliers start: 42 outliers final: 33 residues processed: 184 average time/residue: 0.0794 time to fit residues: 20.3651 Evaluate side-chains 182 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN C 112 GLN E 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.068376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.051225 restraints weight = 32356.047| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.99 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7621 Z= 0.144 Angle : 0.878 14.572 10299 Z= 0.400 Chirality : 0.049 0.403 1143 Planarity : 0.005 0.053 1310 Dihedral : 7.518 59.482 1043 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.88 % Allowed : 29.88 % Favored : 66.25 % 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: 1.27 (0.29), residues: 916 helix: 2.57 (0.28), residues: 316 sheet: 1.08 (0.26), residues: 372 loop : -2.22 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.015 0.001 TYR A 129 PHE 0.021 0.001 PHE E 41 TRP 0.009 0.001 TRP G 54 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7621) covalent geometry : angle 0.87824 / 0.40 (10299) hydrogen bonds : bond 0.04146 / 2.90 ( 518) hydrogen bonds : angle 4.82199 / 3.30 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8614 (ttm170) cc_final: 0.8243 (ttm110) REVERT: A 128 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7534 (t0) REVERT: A 154 MET cc_start: 0.8570 (ttt) cc_final: 0.8075 (tpt) REVERT: A 280 ASP cc_start: 0.9008 (p0) cc_final: 0.8665 (p0) REVERT: B 88 ARG cc_start: 0.8612 (ttm170) cc_final: 0.8243 (ttm110) REVERT: B 154 MET cc_start: 0.8373 (ttt) cc_final: 0.7748 (tpt) REVERT: B 198 ASP cc_start: 0.9288 (p0) cc_final: 0.8959 (t0) REVERT: B 267 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: B 280 ASP cc_start: 0.9021 (p0) cc_final: 0.8670 (p0) REVERT: B 322 TRP cc_start: 0.8913 (m100) cc_final: 0.8295 (m100) REVERT: C 85 LEU cc_start: 0.8790 (tp) cc_final: 0.8446 (pp) REVERT: C 97 LEU cc_start: 0.9342 (tp) cc_final: 0.8690 (tp) REVERT: C 101 PHE cc_start: 0.9338 (m-80) cc_final: 0.8959 (m-80) REVERT: I 34 TYR cc_start: 0.9163 (t80) cc_final: 0.8926 (t80) REVERT: I 38 LEU cc_start: 0.9227 (mm) cc_final: 0.8865 (mm) outliers start: 31 outliers final: 22 residues processed: 187 average time/residue: 0.0802 time to fit residues: 20.6829 Evaluate side-chains 182 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 45 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.067870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.050711 restraints weight = 33168.664| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 5.03 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7621 Z= 0.176 Angle : 0.920 15.543 10299 Z= 0.419 Chirality : 0.049 0.397 1143 Planarity : 0.005 0.054 1310 Dihedral : 7.429 59.172 1041 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.88 % Allowed : 30.62 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.29), residues: 916 helix: 2.53 (0.28), residues: 316 sheet: 1.03 (0.26), residues: 374 loop : -2.13 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.015 0.002 TYR A 129 PHE 0.022 0.002 PHE E 41 TRP 0.009 0.001 TRP E 57 HIS 0.003 0.001 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 7621) covalent geometry : angle 0.92015 / 0.42 (10299) hydrogen bonds : bond 0.04261 / 2.97 ( 518) hydrogen bonds : angle 4.84712 / 3.31 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7515 (t0) REVERT: A 280 ASP cc_start: 0.9032 (p0) cc_final: 0.8691 (p0) REVERT: B 198 ASP cc_start: 0.9290 (p0) cc_final: 0.8946 (t0) REVERT: B 280 ASP cc_start: 0.9046 (p0) cc_final: 0.8694 (p0) REVERT: B 322 TRP cc_start: 0.8897 (m100) cc_final: 0.8285 (m100) REVERT: C 85 LEU cc_start: 0.8758 (tp) cc_final: 0.8421 (pp) REVERT: C 97 LEU cc_start: 0.9358 (tp) cc_final: 0.8691 (tp) REVERT: C 101 PHE cc_start: 0.9365 (m-80) cc_final: 0.8964 (m-80) REVERT: I 23 ASP cc_start: 0.9270 (m-30) cc_final: 0.9008 (p0) REVERT: I 34 TYR cc_start: 0.9176 (t80) cc_final: 0.8954 (t80) REVERT: I 38 LEU cc_start: 0.9251 (mm) cc_final: 0.8903 (mm) outliers start: 31 outliers final: 25 residues processed: 176 average time/residue: 0.0815 time to fit residues: 19.6888 Evaluate side-chains 180 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 45 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 41 optimal weight: 0.0870 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.067959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.050916 restraints weight = 32610.386| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.99 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7621 Z= 0.162 Angle : 0.926 15.546 10299 Z= 0.421 Chirality : 0.050 0.403 1143 Planarity : 0.005 0.053 1310 Dihedral : 7.354 58.336 1041 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 3.50 % Allowed : 31.25 % Favored : 65.25 % 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: 1.29 (0.29), residues: 916 helix: 2.52 (0.28), residues: 316 sheet: 1.07 (0.26), residues: 374 loop : -2.09 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 88 TYR 0.015 0.001 TYR A 129 PHE 0.022 0.001 PHE E 41 TRP 0.008 0.001 TRP G 54 HIS 0.004 0.001 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 7621) covalent geometry : angle 0.92587 / 0.42 (10299) hydrogen bonds : bond 0.04153 / 2.90 ( 518) hydrogen bonds : angle 4.81754 / 3.30 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7495 (t0) REVERT: A 154 MET cc_start: 0.8426 (ttt) cc_final: 0.7801 (tpt) REVERT: A 280 ASP cc_start: 0.9025 (p0) cc_final: 0.8680 (p0) REVERT: B 198 ASP cc_start: 0.9283 (p0) cc_final: 0.8928 (t0) REVERT: B 270 MET cc_start: 0.8200 (mpp) cc_final: 0.7999 (mpp) REVERT: B 280 ASP cc_start: 0.8998 (p0) cc_final: 0.8624 (p0) REVERT: B 322 TRP cc_start: 0.8906 (m100) cc_final: 0.8307 (m100) REVERT: C 85 LEU cc_start: 0.8736 (tp) cc_final: 0.8402 (pp) REVERT: C 97 LEU cc_start: 0.9347 (tp) cc_final: 0.8678 (tp) REVERT: C 101 PHE cc_start: 0.9348 (m-80) cc_final: 0.8959 (m-80) REVERT: I 23 ASP cc_start: 0.9269 (m-30) cc_final: 0.9000 (p0) REVERT: I 34 TYR cc_start: 0.9181 (t80) cc_final: 0.8960 (t80) REVERT: I 38 LEU cc_start: 0.9243 (mm) cc_final: 0.8902 (mm) outliers start: 28 outliers final: 25 residues processed: 171 average time/residue: 0.0818 time to fit residues: 19.3124 Evaluate side-chains 178 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.067616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.050388 restraints weight = 32946.328| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.01 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7621 Z= 0.192 Angle : 0.955 15.760 10299 Z= 0.442 Chirality : 0.050 0.402 1143 Planarity : 0.005 0.053 1310 Dihedral : 7.405 57.496 1041 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.88 % Favored : 93.01 % Rotamer: Outliers : 3.62 % Allowed : 31.62 % Favored : 64.75 % 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: 1.15 (0.29), residues: 916 helix: 2.34 (0.28), residues: 316 sheet: 1.01 (0.26), residues: 374 loop : -2.06 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 88 TYR 0.017 0.002 TYR J 34 PHE 0.022 0.002 PHE E 41 TRP 0.008 0.001 TRP E 57 HIS 0.004 0.001 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 7621) covalent geometry : angle 0.95455 / 0.44 (10299) hydrogen bonds : bond 0.04346 / 2.98 ( 518) hydrogen bonds : angle 4.91413 / 3.37 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7517 (t0) REVERT: A 280 ASP cc_start: 0.9054 (p0) cc_final: 0.8711 (p0) REVERT: B 198 ASP cc_start: 0.9276 (p0) cc_final: 0.8933 (t0) REVERT: B 280 ASP cc_start: 0.9022 (p0) cc_final: 0.8653 (p0) REVERT: B 294 MET cc_start: 0.9275 (tmm) cc_final: 0.9008 (tmm) REVERT: B 322 TRP cc_start: 0.8962 (m100) cc_final: 0.8321 (m100) REVERT: C 97 LEU cc_start: 0.9355 (tp) cc_final: 0.9072 (tp) outliers start: 29 outliers final: 25 residues processed: 167 average time/residue: 0.0809 time to fit residues: 18.6203 Evaluate side-chains 174 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** 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 = 0.3784 r_free = 0.3784 target = 0.067300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.050124 restraints weight = 34038.313| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 4.99 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7621 Z= 0.234 Angle : 0.978 15.251 10299 Z= 0.461 Chirality : 0.052 0.394 1143 Planarity : 0.005 0.057 1310 Dihedral : 7.565 57.798 1041 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.64 % Favored : 92.25 % Rotamer: Outliers : 4.00 % Allowed : 31.50 % Favored : 64.50 % 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: 0.91 (0.29), residues: 916 helix: 2.11 (0.28), residues: 316 sheet: 0.87 (0.26), residues: 376 loop : -2.17 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 88 TYR 0.018 0.002 TYR A 129 PHE 0.024 0.002 PHE E 41 TRP 0.008 0.002 TRP B 259 HIS 0.005 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 ( 7621) covalent geometry : angle 0.97813 / 0.46 (10299) hydrogen bonds : bond 0.04554 / 3.14 ( 518) hydrogen bonds : angle 5.10366 / 3.50 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1939.53 seconds wall clock time: 34 minutes 7.13 seconds (2047.13 seconds total)