Starting phenix.real_space_refine on Tue Feb 3 22:31:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxv_61881/02_2026/9jxv_61881.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxv_61881/02_2026/9jxv_61881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jxv_61881/02_2026/9jxv_61881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxv_61881/02_2026/9jxv_61881.map" model { file = "/net/cci-nas-00/data/ceres_data/9jxv_61881/02_2026/9jxv_61881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxv_61881/02_2026/9jxv_61881.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.061 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 36 5.16 5 C 4770 2.51 5 N 1263 2.21 5 O 1320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7390 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2193 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain: "B" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2193 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain: "C" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 380 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "D" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 380 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "F" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "G" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 409 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "H" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 409 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "J" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 304 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "C" 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: 1.19, per 1000 atoms: 0.16 Number of scatterers: 7390 At special positions: 0 Unit cell: (88.7644, 115.561, 131.472, 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 36 16.00 P 1 15.00 O 1320 8.00 N 1263 7.00 C 4770 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: 0.60 Conformation dependent library (CDL) restraints added in 212.5 milliseconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 2 sheets defined 35.3% alpha, 37.6% 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 82 through 86 removed outlier: 3.572A pdb=" N GLU A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.718A pdb=" N CYS B 86 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'C' and resid 66 through 69 removed outlier: 3.555A pdb=" N LEU C 69 " --> pdb=" O THR C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 66 through 69' Processing helix chain 'C' and resid 70 through 96 removed outlier: 3.887A pdb=" N PHE C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'D' and resid 67 through 96 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.686A pdb=" N LEU E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 61 removed outlier: 3.719A pdb=" N ASN E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 36 removed outlier: 3.875A pdb=" N LEU F 28 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 61 Processing helix chain 'G' and resid 6 through 39 removed outlier: 5.472A 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 49 through 53 Processing helix chain 'H' and resid 6 through 38 removed outlier: 5.336A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Proline residue: H 29 - end of helix removed outlier: 4.050A pdb=" N ARG H 38 " --> pdb=" O LEU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'I' and resid 14 through 48 removed outlier: 3.599A pdb=" N ARG I 18 " --> pdb=" O GLU I 14 " (cutoff:3.500A) Proline residue: I 42 - end of helix Processing helix chain 'J' and resid 14 through 48 Proline residue: J 42 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 110 removed outlier: 6.413A pdb=" N PHE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN A 181 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 329 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A 337 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 110 removed outlier: 6.296A pdb=" N PHE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN B 181 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N PHE B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1536 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: 0.78 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1211 1.32 - 1.45: 1999 1.45 - 1.57: 4277 1.57 - 1.69: 2 1.69 - 1.82: 62 Bond restraints: 7551 Sorted by residual: bond pdb=" C11 PC1 C 201 " pdb=" O13 PC1 C 201 " ideal model delta sigma weight residual 1.407 1.455 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" O13 PC1 C 201 " pdb=" P PC1 C 201 " ideal model delta sigma weight residual 1.652 1.606 0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" C3G PC1 C 201 " pdb=" C3H PC1 C 201 " ideal model delta sigma weight residual 1.524 1.482 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" O11 PC1 C 201 " pdb=" P PC1 C 201 " ideal model delta sigma weight residual 1.642 1.602 0.040 2.00e-02 2.50e+03 3.92e+00 bond pdb=" C2H PC1 C 201 " pdb=" C2I PC1 C 201 " ideal model delta sigma weight residual 1.522 1.485 0.037 2.00e-02 2.50e+03 3.40e+00 ... (remaining 7546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 10031 2.06 - 4.11: 127 4.11 - 6.17: 32 6.17 - 8.22: 8 8.22 - 10.28: 3 Bond angle restraints: 10201 Sorted by residual: angle pdb=" CB LYS H 6 " pdb=" CG LYS H 6 " pdb=" CD LYS H 6 " ideal model delta sigma weight residual 111.30 121.58 -10.28 2.30e+00 1.89e-01 2.00e+01 angle pdb=" CA GLU I 22 " pdb=" CB GLU I 22 " pdb=" CG GLU I 22 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CA MET J 16 " pdb=" CB MET J 16 " pdb=" CG MET J 16 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 angle pdb=" C GLU J 22 " pdb=" N ASP J 23 " pdb=" CA ASP J 23 " ideal model delta sigma weight residual 120.31 114.54 5.77 1.52e+00 4.33e-01 1.44e+01 angle pdb=" N PRO B 333 " pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 110.70 114.82 -4.12 1.22e+00 6.72e-01 1.14e+01 ... (remaining 10196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 3731 18.18 - 36.35: 500 36.35 - 54.53: 189 54.53 - 72.70: 45 72.70 - 90.88: 11 Dihedral angle restraints: 4476 sinusoidal: 1826 harmonic: 2650 Sorted by residual: dihedral pdb=" CA LEU B 332 " pdb=" C LEU B 332 " pdb=" N PRO B 333 " pdb=" CA PRO B 333 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA SER F 63 " pdb=" C SER F 63 " pdb=" N ASP F 64 " pdb=" CA ASP F 64 " ideal model delta harmonic sigma weight residual -180.00 -163.22 -16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP A 306 " pdb=" CB ASP A 306 " pdb=" CG ASP A 306 " pdb=" OD1 ASP A 306 " ideal model delta sinusoidal sigma weight residual -30.00 -87.65 57.65 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 4473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 768 0.036 - 0.072: 259 0.072 - 0.108: 77 0.108 - 0.144: 25 0.144 - 0.180: 6 Chirality restraints: 1135 Sorted by residual: chirality pdb=" CA GLU I 22 " pdb=" N GLU I 22 " pdb=" C GLU I 22 " pdb=" CB GLU I 22 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA ILE A 216 " pdb=" N ILE A 216 " pdb=" C ILE A 216 " pdb=" CB ILE A 216 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 1132 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 169 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO B 170 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 169 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 170 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 101 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C PHE D 101 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE D 101 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU D 102 " 0.011 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 546 2.74 - 3.28: 6619 3.28 - 3.82: 11887 3.82 - 4.36: 13361 4.36 - 4.90: 24970 Nonbonded interactions: 57383 Sorted by model distance: nonbonded pdb=" OH TYR A 237 " pdb=" OE2 GLU A 244 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU A 289 " pdb=" OG SER A 298 " model vdw 2.307 3.040 nonbonded pdb=" O ASN F 39 " pdb=" ND2 ASN F 39 " model vdw 2.314 3.120 nonbonded pdb=" O GLU I 22 " pdb=" OG SER I 26 " model vdw 2.340 3.040 nonbonded pdb=" ND1 HIS A 117 " pdb=" OH TYR A 129 " model vdw 2.369 3.120 ... (remaining 57378 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 66 through 111) 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: 1.930 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.870 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.003 0.048 7551 Z= 0.161 Angle : 0.668 10.280 10201 Z= 0.343 Chirality : 0.043 0.180 1135 Planarity : 0.005 0.058 1290 Dihedral : 19.469 90.880 2776 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.91 % Allowed : 36.58 % Favored : 60.51 % 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: 1.90 (0.30), residues: 914 helix: 2.62 (0.30), residues: 303 sheet: 1.01 (0.27), residues: 384 loop : -0.15 (0.46), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 18 TYR 0.006 0.001 TYR A 237 PHE 0.032 0.001 PHE D 72 TRP 0.009 0.001 TRP E 57 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7551) covalent geometry : angle 0.66765 (10201) hydrogen bonds : bond 0.11010 ( 537) hydrogen bonds : angle 5.73259 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.241 Fit side-chains REVERT: A 200 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8482 (m) REVERT: A 217 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8349 (tt) REVERT: A 260 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8587 (tt) REVERT: A 329 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: B 91 LYS cc_start: 0.8591 (ttmm) cc_final: 0.7775 (tmmt) REVERT: B 107 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8495 (ptpp) REVERT: B 173 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7784 (ttm170) REVERT: B 225 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8247 (mp) REVERT: B 351 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7569 (mmmt) REVERT: C 108 MET cc_start: 0.8445 (tpt) cc_final: 0.8198 (ttm) REVERT: D 75 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.5868 (mm110) REVERT: D 79 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7085 (mtp85) REVERT: G 38 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8251 (tmt-80) REVERT: J 27 SER cc_start: 0.8413 (m) cc_final: 0.8119 (m) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 0.4492 time to fit residues: 66.4597 Evaluate side-chains 131 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain H residue 15 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 ASN F 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121384 restraints weight = 8205.906| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.19 r_work: 0.3240 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7551 Z= 0.137 Angle : 0.609 11.679 10201 Z= 0.311 Chirality : 0.042 0.161 1135 Planarity : 0.005 0.050 1290 Dihedral : 9.882 72.385 1074 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.96 % Allowed : 31.14 % Favored : 61.90 % 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: 2.13 (0.30), residues: 914 helix: 3.00 (0.30), residues: 305 sheet: 1.03 (0.27), residues: 384 loop : -0.12 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 18 TYR 0.019 0.001 TYR G 33 PHE 0.018 0.001 PHE J 43 TRP 0.010 0.001 TRP E 57 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7551) covalent geometry : angle 0.60861 (10201) hydrogen bonds : bond 0.03475 ( 537) hydrogen bonds : angle 4.51777 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 0.296 Fit side-chains REVERT: A 217 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8635 (tt) REVERT: B 107 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8556 (ptpp) REVERT: B 173 ARG cc_start: 0.8313 (ttm170) cc_final: 0.8099 (ttm170) REVERT: B 351 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7683 (mmmt) REVERT: C 71 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6440 (tt) REVERT: C 77 MET cc_start: 0.7456 (tmt) cc_final: 0.6498 (mmt) REVERT: C 108 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8090 (ttm) REVERT: D 75 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.5882 (mm110) REVERT: D 79 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7085 (mtp85) REVERT: E 36 THR cc_start: 0.7692 (m) cc_final: 0.7339 (t) REVERT: G 38 ARG cc_start: 0.8420 (mmm-85) cc_final: 0.8003 (tmt-80) REVERT: G 46 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6680 (mm-30) REVERT: J 20 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7711 (mpt) REVERT: J 27 SER cc_start: 0.8271 (m) cc_final: 0.7914 (m) outliers start: 55 outliers final: 25 residues processed: 166 average time/residue: 0.5329 time to fit residues: 92.9871 Evaluate side-chains 142 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 257 ASN F 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123059 restraints weight = 8187.318| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.49 r_work: 0.3160 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7551 Z= 0.189 Angle : 0.645 13.850 10201 Z= 0.330 Chirality : 0.044 0.169 1135 Planarity : 0.005 0.050 1290 Dihedral : 8.671 71.794 1053 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 8.35 % Allowed : 29.75 % Favored : 61.90 % 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: 2.05 (0.29), residues: 914 helix: 3.01 (0.30), residues: 305 sheet: 0.97 (0.27), residues: 392 loop : -0.30 (0.46), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 240 TYR 0.009 0.001 TYR B 275 PHE 0.020 0.002 PHE A 356 TRP 0.012 0.001 TRP B 259 HIS 0.005 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 7551) covalent geometry : angle 0.64531 (10201) hydrogen bonds : bond 0.03546 ( 537) hydrogen bonds : angle 4.45150 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 118 time to evaluate : 0.267 Fit side-chains REVERT: A 193 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: A 200 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8479 (m) REVERT: A 217 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8725 (tt) REVERT: B 107 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8689 (ptpp) REVERT: B 173 ARG cc_start: 0.8278 (ttm170) cc_final: 0.8052 (ttm170) REVERT: B 180 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8353 (t) REVERT: B 193 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: B 225 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 294 MET cc_start: 0.8758 (mmt) cc_final: 0.8372 (mmm) REVERT: B 351 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7673 (mmmt) REVERT: C 71 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6434 (tt) REVERT: C 77 MET cc_start: 0.7467 (tmt) cc_final: 0.6423 (mmt) REVERT: C 108 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8055 (ttm) REVERT: D 75 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.5846 (mm110) REVERT: D 79 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7022 (mmp80) REVERT: E 36 THR cc_start: 0.7743 (m) cc_final: 0.7368 (t) REVERT: E 42 ARG cc_start: 0.8185 (mtm110) cc_final: 0.7842 (mpp-170) REVERT: F 28 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5512 (pp) REVERT: G 38 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.8013 (tmt-80) REVERT: G 46 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6658 (mm-30) REVERT: J 20 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7661 (mpt) REVERT: J 27 SER cc_start: 0.8287 (m) cc_final: 0.7990 (m) REVERT: J 37 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7433 (tt) REVERT: J 47 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6562 (tmmm) outliers start: 66 outliers final: 35 residues processed: 167 average time/residue: 0.4037 time to fit residues: 71.8717 Evaluate side-chains 164 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 47 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN B 304 GLN D 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123666 restraints weight = 8254.326| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.58 r_work: 0.3161 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7551 Z= 0.171 Angle : 0.623 13.550 10201 Z= 0.319 Chirality : 0.043 0.167 1135 Planarity : 0.005 0.052 1290 Dihedral : 8.561 69.805 1053 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 8.73 % Allowed : 29.11 % Favored : 62.15 % 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: 2.07 (0.29), residues: 914 helix: 3.08 (0.29), residues: 305 sheet: 0.95 (0.27), residues: 392 loop : -0.34 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.020 0.001 TYR G 33 PHE 0.022 0.002 PHE J 43 TRP 0.010 0.001 TRP B 259 HIS 0.007 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7551) covalent geometry : angle 0.62277 (10201) hydrogen bonds : bond 0.03339 ( 537) hydrogen bonds : angle 4.39293 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 125 time to evaluate : 0.231 Fit side-chains REVERT: A 193 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: A 200 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8449 (m) REVERT: A 217 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8760 (tt) REVERT: A 260 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 280 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8111 (t0) REVERT: B 107 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8825 (ptpp) REVERT: B 163 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: B 173 ARG cc_start: 0.8275 (ttm170) cc_final: 0.8054 (ttm170) REVERT: B 180 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8308 (t) REVERT: B 193 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: B 225 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8316 (mp) REVERT: B 294 MET cc_start: 0.8779 (mmt) cc_final: 0.8514 (mmm) REVERT: B 351 LYS cc_start: 0.8100 (mmtm) cc_final: 0.7632 (mmmt) REVERT: C 71 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6420 (tp) REVERT: C 77 MET cc_start: 0.7477 (tmt) cc_final: 0.6437 (mmt) REVERT: D 79 ARG cc_start: 0.7998 (mtm180) cc_final: 0.7026 (mmp80) REVERT: E 36 THR cc_start: 0.7767 (m) cc_final: 0.7410 (t) REVERT: E 42 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7844 (mpp-170) REVERT: F 26 ASP cc_start: 0.4696 (OUTLIER) cc_final: 0.3927 (m-30) REVERT: F 28 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5509 (pp) REVERT: G 38 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.7985 (tmt-80) REVERT: G 46 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6678 (mm-30) REVERT: J 20 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7656 (mpt) REVERT: J 27 SER cc_start: 0.8352 (m) cc_final: 0.8019 (m) REVERT: J 47 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6568 (tmmm) outliers start: 69 outliers final: 37 residues processed: 177 average time/residue: 0.4322 time to fit residues: 80.8668 Evaluate side-chains 166 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 113 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 47 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 53 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.0670 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 41 optimal weight: 0.0030 chunk 50 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126034 restraints weight = 8276.586| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.55 r_work: 0.3203 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7551 Z= 0.106 Angle : 0.582 11.625 10201 Z= 0.299 Chirality : 0.042 0.167 1135 Planarity : 0.004 0.053 1290 Dihedral : 8.184 65.978 1050 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.84 % Allowed : 31.01 % Favored : 62.15 % 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: 2.20 (0.30), residues: 914 helix: 3.22 (0.30), residues: 305 sheet: 1.00 (0.27), residues: 382 loop : -0.19 (0.45), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 29 TYR 0.007 0.001 TYR A 237 PHE 0.015 0.001 PHE A 356 TRP 0.010 0.001 TRP F 57 HIS 0.007 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7551) covalent geometry : angle 0.58157 (10201) hydrogen bonds : bond 0.02888 ( 537) hydrogen bonds : angle 4.27701 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 0.201 Fit side-chains REVERT: A 200 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8389 (m) REVERT: A 217 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8634 (tt) REVERT: B 107 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8865 (ptpp) REVERT: B 163 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: B 180 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8168 (t) REVERT: B 193 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: B 294 MET cc_start: 0.8795 (mmt) cc_final: 0.8546 (mmm) REVERT: B 351 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7581 (mmmt) REVERT: C 77 MET cc_start: 0.7482 (tmt) cc_final: 0.6413 (mmt) REVERT: D 79 ARG cc_start: 0.7948 (mtm180) cc_final: 0.6973 (mmp80) REVERT: E 36 THR cc_start: 0.7761 (m) cc_final: 0.7419 (t) REVERT: E 42 ARG cc_start: 0.8127 (mtm110) cc_final: 0.7913 (mpp-170) REVERT: F 26 ASP cc_start: 0.4655 (OUTLIER) cc_final: 0.3908 (m-30) REVERT: F 28 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.5456 (pp) REVERT: F 65 ILE cc_start: 0.4803 (OUTLIER) cc_final: 0.4201 (tt) REVERT: G 38 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.7962 (tmt-80) REVERT: G 46 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6642 (mm-30) REVERT: J 20 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7571 (mpt) REVERT: J 27 SER cc_start: 0.8371 (m) cc_final: 0.8029 (m) REVERT: J 37 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7418 (tt) REVERT: J 47 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6575 (tmmm) outliers start: 54 outliers final: 25 residues processed: 160 average time/residue: 0.4534 time to fit residues: 76.8682 Evaluate side-chains 159 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 47 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125887 restraints weight = 8233.641| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.62 r_work: 0.3190 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7551 Z= 0.126 Angle : 0.587 11.636 10201 Z= 0.301 Chirality : 0.042 0.168 1135 Planarity : 0.004 0.052 1290 Dihedral : 8.052 66.642 1049 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 7.22 % Allowed : 31.01 % Favored : 61.77 % 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: 2.22 (0.30), residues: 914 helix: 3.25 (0.30), residues: 305 sheet: 0.99 (0.27), residues: 384 loop : -0.16 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 240 TYR 0.023 0.001 TYR G 33 PHE 0.023 0.001 PHE J 43 TRP 0.010 0.001 TRP F 57 HIS 0.008 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7551) covalent geometry : angle 0.58703 (10201) hydrogen bonds : bond 0.02968 ( 537) hydrogen bonds : angle 4.21328 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 200 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8417 (m) REVERT: A 217 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8704 (tt) REVERT: A 260 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8669 (tt) REVERT: B 107 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8847 (ptpp) REVERT: B 163 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: B 173 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7666 (ttm170) REVERT: B 180 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8246 (t) REVERT: B 193 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: B 225 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 294 MET cc_start: 0.8816 (mmt) cc_final: 0.8570 (mmm) REVERT: B 351 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7655 (mmmt) REVERT: C 77 MET cc_start: 0.7525 (tmt) cc_final: 0.6489 (mmt) REVERT: D 79 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7036 (mmp80) REVERT: E 36 THR cc_start: 0.7813 (m) cc_final: 0.7468 (t) REVERT: E 42 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7914 (mpp-170) REVERT: F 26 ASP cc_start: 0.4738 (OUTLIER) cc_final: 0.3896 (m-30) REVERT: F 28 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.5515 (pp) REVERT: F 65 ILE cc_start: 0.4802 (OUTLIER) cc_final: 0.4196 (tt) REVERT: G 38 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7958 (tmt-80) REVERT: G 46 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6678 (mm-30) REVERT: J 27 SER cc_start: 0.8451 (m) cc_final: 0.8099 (m) REVERT: J 37 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7480 (tt) REVERT: J 47 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6575 (tmmm) outliers start: 57 outliers final: 32 residues processed: 171 average time/residue: 0.4425 time to fit residues: 80.1427 Evaluate side-chains 162 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 47 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.169742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118035 restraints weight = 8219.680| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.29 r_work: 0.3203 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7551 Z= 0.125 Angle : 0.599 11.517 10201 Z= 0.306 Chirality : 0.043 0.173 1135 Planarity : 0.004 0.052 1290 Dihedral : 8.004 65.760 1049 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 7.59 % Allowed : 30.89 % Favored : 61.52 % 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: 2.23 (0.30), residues: 914 helix: 3.23 (0.30), residues: 305 sheet: 1.01 (0.27), residues: 384 loop : -0.17 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 239 TYR 0.007 0.001 TYR A 237 PHE 0.016 0.001 PHE A 356 TRP 0.010 0.001 TRP F 57 HIS 0.008 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7551) covalent geometry : angle 0.59888 (10201) hydrogen bonds : bond 0.02976 ( 537) hydrogen bonds : angle 4.21326 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 116 time to evaluate : 0.246 Fit side-chains REVERT: A 191 ASP cc_start: 0.7815 (m-30) cc_final: 0.7582 (t70) REVERT: A 200 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8397 (m) REVERT: A 217 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8692 (tt) REVERT: A 260 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8659 (tt) REVERT: B 163 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: B 173 ARG cc_start: 0.8278 (ttm170) cc_final: 0.7811 (ttm170) REVERT: B 180 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8251 (t) REVERT: B 193 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: B 225 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8341 (mp) REVERT: B 294 MET cc_start: 0.8822 (mmt) cc_final: 0.8571 (mmm) REVERT: B 351 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7648 (mmmt) REVERT: C 77 MET cc_start: 0.7493 (tmt) cc_final: 0.6453 (mmt) REVERT: D 79 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7014 (mmp80) REVERT: E 36 THR cc_start: 0.7817 (m) cc_final: 0.7481 (t) REVERT: F 26 ASP cc_start: 0.4611 (OUTLIER) cc_final: 0.3788 (m-30) REVERT: F 28 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5564 (pp) REVERT: F 65 ILE cc_start: 0.4763 (OUTLIER) cc_final: 0.4153 (tt) REVERT: G 38 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7955 (tmt-80) REVERT: G 46 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: J 20 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7495 (mpt) REVERT: J 27 SER cc_start: 0.8404 (m) cc_final: 0.8023 (m) REVERT: J 37 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7484 (tt) REVERT: J 47 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6590 (tmmm) outliers start: 60 outliers final: 35 residues processed: 164 average time/residue: 0.4019 time to fit residues: 70.3633 Evaluate side-chains 163 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 47 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 0.0040 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.171101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128343 restraints weight = 8263.771| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.36 r_work: 0.3235 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7551 Z= 0.127 Angle : 0.599 11.511 10201 Z= 0.307 Chirality : 0.043 0.169 1135 Planarity : 0.004 0.052 1290 Dihedral : 7.874 65.299 1045 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 7.47 % Allowed : 31.27 % Favored : 61.27 % 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: 2.21 (0.29), residues: 914 helix: 3.20 (0.30), residues: 305 sheet: 1.02 (0.27), residues: 384 loop : -0.19 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 38 TYR 0.024 0.001 TYR G 33 PHE 0.024 0.001 PHE J 43 TRP 0.010 0.001 TRP F 57 HIS 0.008 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7551) covalent geometry : angle 0.59943 (10201) hydrogen bonds : bond 0.02955 ( 537) hydrogen bonds : angle 4.21254 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 200 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8438 (m) REVERT: A 217 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8756 (tt) REVERT: A 239 ARG cc_start: 0.8378 (ttm-80) cc_final: 0.7890 (ttm-80) REVERT: A 260 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8680 (tt) REVERT: B 163 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: B 173 ARG cc_start: 0.8322 (ttm170) cc_final: 0.7946 (ttm170) REVERT: B 180 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8286 (t) REVERT: B 193 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: B 225 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8364 (mp) REVERT: B 294 MET cc_start: 0.8811 (mmt) cc_final: 0.8562 (mmm) REVERT: B 351 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7687 (mmmt) REVERT: C 77 MET cc_start: 0.7477 (tmt) cc_final: 0.6441 (mmt) REVERT: E 36 THR cc_start: 0.7841 (m) cc_final: 0.7503 (t) REVERT: F 26 ASP cc_start: 0.4576 (OUTLIER) cc_final: 0.3761 (m-30) REVERT: F 28 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5578 (pp) REVERT: F 65 ILE cc_start: 0.4680 (OUTLIER) cc_final: 0.4084 (tt) REVERT: G 38 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7921 (tmt-80) REVERT: G 46 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: I 25 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8899 (pp) REVERT: J 20 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7594 (mpt) REVERT: J 25 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8732 (mt) REVERT: J 27 SER cc_start: 0.8439 (m) cc_final: 0.8059 (m) REVERT: J 47 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6576 (tmmm) outliers start: 59 outliers final: 35 residues processed: 178 average time/residue: 0.4107 time to fit residues: 77.5626 Evaluate side-chains 167 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 47 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 65 optimal weight: 0.4980 chunk 27 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.172111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128953 restraints weight = 8192.010| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.37 r_work: 0.3243 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7551 Z= 0.113 Angle : 0.596 10.989 10201 Z= 0.304 Chirality : 0.043 0.214 1135 Planarity : 0.004 0.052 1290 Dihedral : 7.785 63.262 1045 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 7.59 % Allowed : 31.27 % Favored : 61.14 % 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: 2.21 (0.30), residues: 914 helix: 3.17 (0.30), residues: 305 sheet: 0.95 (0.27), residues: 400 loop : -0.07 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 38 TYR 0.006 0.001 TYR A 237 PHE 0.016 0.001 PHE D 72 TRP 0.011 0.001 TRP F 57 HIS 0.008 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7551) covalent geometry : angle 0.59559 (10201) hydrogen bonds : bond 0.02825 ( 537) hydrogen bonds : angle 4.16487 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 118 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 200 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8452 (m) REVERT: A 217 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 239 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.7903 (ttm-80) REVERT: A 240 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7744 (ttp-170) REVERT: B 163 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: B 173 ARG cc_start: 0.8333 (ttm170) cc_final: 0.7952 (ttm170) REVERT: B 180 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8244 (t) REVERT: B 193 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: B 294 MET cc_start: 0.8822 (mmt) cc_final: 0.8571 (mmm) REVERT: B 351 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7721 (mmmt) REVERT: C 77 MET cc_start: 0.7537 (tmt) cc_final: 0.6505 (mmt) REVERT: E 36 THR cc_start: 0.7858 (m) cc_final: 0.7518 (t) REVERT: F 26 ASP cc_start: 0.4590 (OUTLIER) cc_final: 0.3777 (m-30) REVERT: F 28 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5602 (pp) REVERT: F 65 ILE cc_start: 0.4670 (OUTLIER) cc_final: 0.4052 (tt) REVERT: G 19 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8614 (p) REVERT: G 38 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.7947 (tmt-80) REVERT: G 46 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6660 (mm-30) REVERT: I 25 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8917 (pp) REVERT: J 20 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7629 (mpp) REVERT: J 25 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8702 (mt) REVERT: J 27 SER cc_start: 0.8455 (m) cc_final: 0.8040 (m) REVERT: J 47 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6597 (tmmm) outliers start: 60 outliers final: 29 residues processed: 169 average time/residue: 0.4178 time to fit residues: 74.9709 Evaluate side-chains 164 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 47 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS B 116 ASN I 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127966 restraints weight = 8161.922| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.36 r_work: 0.3230 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7551 Z= 0.135 Angle : 0.620 11.105 10201 Z= 0.316 Chirality : 0.044 0.240 1135 Planarity : 0.004 0.051 1290 Dihedral : 7.799 64.237 1045 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 6.58 % Allowed : 31.77 % Favored : 61.65 % 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: 2.17 (0.29), residues: 914 helix: 3.08 (0.30), residues: 305 sheet: 1.06 (0.27), residues: 384 loop : -0.22 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 38 TYR 0.027 0.001 TYR G 33 PHE 0.024 0.001 PHE J 43 TRP 0.010 0.001 TRP F 57 HIS 0.008 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7551) covalent geometry : angle 0.62008 (10201) hydrogen bonds : bond 0.03038 ( 537) hydrogen bonds : angle 4.21756 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 217 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8752 (tt) REVERT: A 239 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: A 240 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7722 (ttp-170) REVERT: B 163 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: B 173 ARG cc_start: 0.8304 (ttm170) cc_final: 0.7939 (ttm170) REVERT: B 180 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8271 (t) REVERT: B 193 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: B 294 MET cc_start: 0.8817 (mmt) cc_final: 0.8560 (mmm) REVERT: B 351 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7712 (mmmt) REVERT: C 77 MET cc_start: 0.7505 (tmt) cc_final: 0.6455 (mmt) REVERT: E 36 THR cc_start: 0.7849 (m) cc_final: 0.7513 (t) REVERT: F 26 ASP cc_start: 0.4648 (OUTLIER) cc_final: 0.3832 (m-30) REVERT: F 28 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5662 (pp) REVERT: F 65 ILE cc_start: 0.4678 (OUTLIER) cc_final: 0.4055 (tt) REVERT: G 38 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7908 (tmt-80) REVERT: G 46 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6662 (mm-30) REVERT: J 25 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8711 (mt) REVERT: J 47 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6611 (tmmt) outliers start: 52 outliers final: 35 residues processed: 164 average time/residue: 0.4542 time to fit residues: 78.7953 Evaluate side-chains 159 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 47 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.0040 chunk 6 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 0.0060 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 64 optimal weight: 0.0170 chunk 4 optimal weight: 3.9990 overall best weight: 0.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS A 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.174616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.131360 restraints weight = 8191.469| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.33 r_work: 0.3284 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 7551 Z= 0.101 Angle : 0.593 9.510 10201 Z= 0.302 Chirality : 0.042 0.224 1135 Planarity : 0.004 0.052 1290 Dihedral : 7.601 59.584 1045 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.68 % Allowed : 34.30 % Favored : 61.01 % 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: 2.22 (0.30), residues: 914 helix: 3.08 (0.30), residues: 305 sheet: 1.06 (0.27), residues: 398 loop : -0.10 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 82 TYR 0.008 0.001 TYR I 34 PHE 0.015 0.001 PHE D 72 TRP 0.010 0.001 TRP F 57 HIS 0.008 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7551) covalent geometry : angle 0.59253 (10201) hydrogen bonds : bond 0.02638 ( 537) hydrogen bonds : angle 4.12872 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2851.03 seconds wall clock time: 49 minutes 5.86 seconds (2945.86 seconds total)