Starting phenix.real_space_refine on Fri Sep 11 23:11:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y00_33536/09_2026/7y00_33536.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y00_33536/09_2026/7y00_33536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y00_33536/09_2026/7y00_33536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y00_33536/09_2026/7y00_33536.map" model { file = "/net/cci-nas-00/data/ceres_data/7y00_33536/09_2026/7y00_33536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y00_33536/09_2026/7y00_33536.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 310 5.49 5 S 14 5.16 5 C 6823 2.51 5 N 2339 2.21 5 O 2925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12411 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3166 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Chain: "J" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3189 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Time building chain proxies: 2.70, per 1000 atoms: 0.22 Number of scatterers: 12411 At special positions: 0 Unit cell: (116.6, 147.34, 113.42, 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 14 16.00 P 310 15.00 O 2925 8.00 N 2339 7.00 C 6823 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: 0.97 Conformation dependent library (CDL) restraints added in 382.9 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.5% alpha, 3.1% beta 153 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.096A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.292A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.117A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.995A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.537A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.553A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.268A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.523A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.757A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.501A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.761A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.342A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.547A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 415 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 395 hydrogen bonds 786 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2627 1.34 - 1.46: 4279 1.46 - 1.57: 5716 1.57 - 1.69: 618 1.69 - 1.81: 24 Bond restraints: 13264 Sorted by residual: bond pdb=" C1' DC I 139 " pdb=" N1 DC I 139 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.35e+01 bond pdb=" C1' DG J 31 " pdb=" N9 DG J 31 " ideal model delta sigma weight residual 1.468 1.391 0.077 1.40e-02 5.10e+03 3.04e+01 bond pdb=" C3' DT J 113 " pdb=" C2' DT J 113 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DA I 133 " pdb=" C2' DA I 133 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG I 124 " pdb=" C2' DG I 124 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 13259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 18058 1.73 - 3.46: 1118 3.46 - 5.19: 44 5.19 - 6.92: 15 6.92 - 8.65: 3 Bond angle restraints: 19238 Sorted by residual: angle pdb=" O4' DA I 89 " pdb=" C4' DA I 89 " pdb=" C3' DA I 89 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.36e+01 angle pdb=" N3 DT J 41 " pdb=" C4 DT J 41 " pdb=" O4 DT J 41 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT J 48 " pdb=" C4 DT J 48 " pdb=" O4 DT J 48 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT J 113 " pdb=" C4 DT J 113 " pdb=" O4 DT J 113 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT J 75 " pdb=" C4 DT J 75 " pdb=" O4 DT J 75 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 19233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4655 17.78 - 35.56: 1125 35.56 - 53.34: 1042 53.34 - 71.13: 324 71.13 - 88.91: 19 Dihedral angle restraints: 7165 sinusoidal: 4961 harmonic: 2204 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " pdb=" CG1 ILE G 87 " pdb=" CD1 ILE G 87 " ideal model delta sinusoidal sigma weight residual 180.00 122.74 57.26 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -138.72 -41.28 2 1.50e+01 4.44e-03 9.29e+00 ... (remaining 7162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1560 0.046 - 0.091: 476 0.091 - 0.137: 133 0.137 - 0.182: 10 0.182 - 0.228: 5 Chirality restraints: 2184 Sorted by residual: chirality pdb=" CA GLU C 61 " pdb=" N GLU C 61 " pdb=" C GLU C 61 " pdb=" CB GLU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 2181 not shown) Planarity restraints: 1361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 52 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C ALA G 52 " 0.077 2.00e-02 2.50e+03 pdb=" O ALA G 52 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA G 53 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C LYS F 59 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 87 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C SER E 87 " -0.028 2.00e-02 2.50e+03 pdb=" O SER E 87 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA E 88 " 0.010 2.00e-02 2.50e+03 ... (remaining 1358 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 27 2.35 - 2.99: 5762 2.99 - 3.63: 21890 3.63 - 4.26: 33094 4.26 - 4.90: 47127 Nonbonded interactions: 107900 Sorted by model distance: nonbonded pdb=" CD1 LEU G 23 " pdb=" OE1 GLU G 56 " model vdw 1.717 3.460 nonbonded pdb=" N GLN G 24 " pdb=" OE2 GLU G 56 " model vdw 2.100 3.120 nonbonded pdb=" O2 DC I 49 " pdb=" N2 DG J 121 " model vdw 2.194 2.496 nonbonded pdb=" OG1 THR G 16 " pdb=" OP1 DA J 55 " model vdw 2.195 3.040 nonbonded pdb=" OG SER D 84 " pdb=" OP1 DG I 38 " model vdw 2.223 3.040 ... (remaining 107895 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 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.490 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 13264 Z= 0.539 Angle : 0.839 8.646 19238 Z= 0.718 Chirality : 0.048 0.228 2184 Planarity : 0.005 0.045 1361 Dihedral : 27.461 88.908 5745 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.31 % Allowed : 1.10 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.28), residues: 746 helix: 1.00 (0.20), residues: 549 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 92 TYR 0.026 0.002 TYR B 88 PHE 0.015 0.002 PHE G 25 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.54 (13264) covalent geometry : angle 0.83851 / 0.72 (19238) hydrogen bonds : bond 0.09614 / 6.72 ( 810) hydrogen bonds : angle 3.85534 / 2.80 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8407 (tm-30) REVERT: B 49 LEU cc_start: 0.9175 (mt) cc_final: 0.8924 (mt) REVERT: B 53 GLU cc_start: 0.8655 (mp0) cc_final: 0.8427 (mp0) REVERT: C 72 ASP cc_start: 0.8941 (m-30) cc_final: 0.8720 (m-30) REVERT: C 90 ASP cc_start: 0.8518 (t0) cc_final: 0.8212 (t70) REVERT: D 42 LEU cc_start: 0.9576 (tp) cc_final: 0.9318 (tp) REVERT: D 65 ASP cc_start: 0.8916 (t0) cc_final: 0.8545 (t0) REVERT: E 62 ILE cc_start: 0.9611 (tt) cc_final: 0.9372 (tt) REVERT: E 74 ILE cc_start: 0.9547 (tt) cc_final: 0.9331 (tt) REVERT: F 63 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8918 (mp0) REVERT: G 64 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8473 (tm-30) REVERT: H 45 VAL cc_start: 0.9002 (t) cc_final: 0.8748 (t) REVERT: H 65 ASP cc_start: 0.9048 (t70) cc_final: 0.8844 (t0) REVERT: H 73 GLU cc_start: 0.9031 (tp30) cc_final: 0.8540 (tp30) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.1089 time to fit residues: 30.6970 Evaluate side-chains 137 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN E 93 GLN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.051317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040274 restraints weight = 130854.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041074 restraints weight = 63288.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.041483 restraints weight = 39670.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041786 restraints weight = 31418.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.042043 restraints weight = 26676.999| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 13264 Z= 0.203 Angle : 0.686 8.612 19238 Z= 0.411 Chirality : 0.043 0.191 2184 Planarity : 0.005 0.057 1361 Dihedral : 31.053 90.272 4224 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.89 % Allowed : 12.76 % Favored : 85.35 % 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: 1.96 (0.30), residues: 746 helix: 1.91 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.42 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.030 0.002 TYR C 50 PHE 0.009 0.001 PHE E 67 HIS 0.008 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 (13264) covalent geometry : angle 0.68617 / 0.41 (19238) hydrogen bonds : bond 0.05628 / 3.87 ( 810) hydrogen bonds : angle 3.35887 / 2.45 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9002 (tt0) cc_final: 0.8274 (tt0) REVERT: A 105 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8597 (tm-30) REVERT: B 49 LEU cc_start: 0.9293 (mt) cc_final: 0.8767 (mt) REVERT: B 53 GLU cc_start: 0.8738 (mp0) cc_final: 0.8377 (mp0) REVERT: B 59 LYS cc_start: 0.9224 (tppp) cc_final: 0.8644 (tppp) REVERT: B 63 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8650 (mp0) REVERT: B 88 TYR cc_start: 0.8919 (m-10) cc_final: 0.8546 (m-10) REVERT: C 90 ASP cc_start: 0.8696 (t0) cc_final: 0.8422 (t70) REVERT: D 65 ASP cc_start: 0.9177 (t0) cc_final: 0.8651 (t0) REVERT: D 68 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8431 (tm-30) REVERT: E 93 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8635 (tp40) REVERT: E 120 MET cc_start: 0.7601 (mtm) cc_final: 0.7108 (mpp) REVERT: F 53 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9282 (mm-30) REVERT: F 93 GLN cc_start: 0.9364 (tp40) cc_final: 0.9079 (tp40) REVERT: G 64 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8710 (tm-30) REVERT: G 104 GLN cc_start: 0.8145 (mp10) cc_final: 0.7809 (mp10) REVERT: H 65 ASP cc_start: 0.9307 (t70) cc_final: 0.9063 (t0) REVERT: H 73 GLU cc_start: 0.9254 (tp30) cc_final: 0.8838 (tp30) outliers start: 12 outliers final: 5 residues processed: 161 average time/residue: 0.1004 time to fit residues: 24.4403 Evaluate side-chains 138 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 78 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.048442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.037227 restraints weight = 133749.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.037987 restraints weight = 64075.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.038404 restraints weight = 40219.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.038704 restraints weight = 31529.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038944 restraints weight = 26866.930| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13264 Z= 0.184 Angle : 0.669 10.739 19238 Z= 0.393 Chirality : 0.043 0.200 2184 Planarity : 0.005 0.055 1361 Dihedral : 31.519 90.149 4224 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.15 % Allowed : 14.49 % Favored : 82.36 % 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: 1.94 (0.30), residues: 746 helix: 1.95 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.59 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.029 0.002 TYR F 88 PHE 0.019 0.002 PHE E 67 HIS 0.007 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 (13264) covalent geometry : angle 0.66901 / 0.39 (19238) hydrogen bonds : bond 0.04903 / 3.39 ( 810) hydrogen bonds : angle 3.24278 / 2.36 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8996 (tt0) cc_final: 0.8341 (tt0) REVERT: A 97 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8469 (mt-10) REVERT: A 105 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8606 (tm-30) REVERT: B 49 LEU cc_start: 0.9359 (mt) cc_final: 0.8818 (mt) REVERT: B 53 GLU cc_start: 0.8871 (mp0) cc_final: 0.8467 (pm20) REVERT: B 63 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: B 74 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 88 TYR cc_start: 0.9001 (m-10) cc_final: 0.8578 (m-10) REVERT: C 61 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8571 (mm-30) REVERT: C 90 ASP cc_start: 0.8818 (t0) cc_final: 0.8539 (t70) REVERT: D 65 ASP cc_start: 0.9171 (t0) cc_final: 0.8675 (t0) REVERT: D 68 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8495 (tm-30) REVERT: E 93 GLN cc_start: 0.9037 (tt0) cc_final: 0.8797 (tp40) REVERT: E 97 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8565 (mt-10) REVERT: E 120 MET cc_start: 0.7757 (mtm) cc_final: 0.7227 (mpp) REVERT: F 93 GLN cc_start: 0.9394 (tp40) cc_final: 0.9174 (tp40) REVERT: G 61 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8855 (mm-30) REVERT: G 104 GLN cc_start: 0.8399 (mp10) cc_final: 0.8120 (mp10) REVERT: H 65 ASP cc_start: 0.9344 (t70) cc_final: 0.9074 (t0) REVERT: H 73 GLU cc_start: 0.9271 (tp30) cc_final: 0.8840 (tp30) REVERT: H 80 TYR cc_start: 0.7453 (m-10) cc_final: 0.7071 (m-10) outliers start: 20 outliers final: 9 residues processed: 164 average time/residue: 0.0935 time to fit residues: 23.2877 Evaluate side-chains 141 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 89 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 50.0000 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.043579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.032363 restraints weight = 134999.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.033072 restraints weight = 64180.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.033424 restraints weight = 40087.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.033704 restraints weight = 31898.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.033956 restraints weight = 27078.608| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 13264 Z= 0.252 Angle : 0.767 13.320 19238 Z= 0.428 Chirality : 0.046 0.326 2184 Planarity : 0.006 0.063 1361 Dihedral : 31.917 89.652 4224 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.99 % Allowed : 16.69 % Favored : 80.31 % 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: 1.45 (0.30), residues: 746 helix: 1.54 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.63 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 39 TYR 0.024 0.002 TYR F 88 PHE 0.015 0.002 PHE G 25 HIS 0.009 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.25 (13264) covalent geometry : angle 0.76715 / 0.43 (19238) hydrogen bonds : bond 0.06745 / 4.61 ( 810) hydrogen bonds : angle 3.63674 / 2.68 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8588 (tm-30) REVERT: B 53 GLU cc_start: 0.8979 (mp0) cc_final: 0.8524 (mp0) REVERT: B 63 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: B 74 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8299 (mt-10) REVERT: B 84 MET cc_start: 0.9332 (mmm) cc_final: 0.8892 (mmm) REVERT: B 88 TYR cc_start: 0.9074 (m-10) cc_final: 0.8484 (m-10) REVERT: C 39 TYR cc_start: 0.9509 (m-80) cc_final: 0.9202 (m-80) REVERT: C 56 GLU cc_start: 0.8842 (tt0) cc_final: 0.8525 (mm-30) REVERT: C 61 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8517 (mm-30) REVERT: C 90 ASP cc_start: 0.8873 (t0) cc_final: 0.8649 (t70) REVERT: D 65 ASP cc_start: 0.9188 (t0) cc_final: 0.8733 (t0) REVERT: D 68 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8533 (tm-30) REVERT: E 76 GLN cc_start: 0.9111 (mp10) cc_final: 0.8834 (mp10) REVERT: E 97 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8368 (mt-10) REVERT: E 120 MET cc_start: 0.8241 (mtm) cc_final: 0.7471 (mpp) REVERT: F 53 GLU cc_start: 0.9237 (mp0) cc_final: 0.8934 (mp0) REVERT: F 84 MET cc_start: 0.8951 (tpp) cc_final: 0.8669 (tpp) REVERT: G 64 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.9055 (pp20) REVERT: G 104 GLN cc_start: 0.8583 (mp10) cc_final: 0.8281 (mp10) REVERT: H 65 ASP cc_start: 0.9318 (t70) cc_final: 0.9096 (t0) REVERT: H 73 GLU cc_start: 0.9360 (tp30) cc_final: 0.8892 (tp30) REVERT: H 102 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8715 (tp30) outliers start: 19 outliers final: 10 residues processed: 152 average time/residue: 0.1016 time to fit residues: 23.0282 Evaluate side-chains 133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 5.9990 chunk 88 optimal weight: 40.0000 chunk 95 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 24 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.044210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032855 restraints weight = 131368.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.033557 restraints weight = 61676.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033934 restraints weight = 38533.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.034222 restraints weight = 30659.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.034503 restraints weight = 26064.285| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13264 Z= 0.150 Angle : 0.655 10.092 19238 Z= 0.378 Chirality : 0.043 0.279 2184 Planarity : 0.004 0.050 1361 Dihedral : 31.879 90.288 4224 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.73 % Allowed : 21.57 % Favored : 76.69 % 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: 746 helix: 1.94 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.036 0.002 TYR F 88 PHE 0.010 0.001 PHE G 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (13264) covalent geometry : angle 0.65536 / 0.38 (19238) hydrogen bonds : bond 0.04369 / 3.04 ( 810) hydrogen bonds : angle 3.21775 / 2.34 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8498 (tm-30) REVERT: B 53 GLU cc_start: 0.8982 (mp0) cc_final: 0.8549 (mp0) REVERT: B 63 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8638 (mp0) REVERT: B 74 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8281 (mt-10) REVERT: B 88 TYR cc_start: 0.9016 (m-10) cc_final: 0.8556 (m-10) REVERT: C 39 TYR cc_start: 0.9515 (m-80) cc_final: 0.9188 (m-80) REVERT: C 56 GLU cc_start: 0.8839 (tt0) cc_final: 0.8564 (mm-30) REVERT: C 90 ASP cc_start: 0.8866 (t0) cc_final: 0.8656 (t70) REVERT: D 65 ASP cc_start: 0.9101 (t0) cc_final: 0.8634 (t0) REVERT: D 68 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8508 (tm-30) REVERT: E 97 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8477 (mt-10) REVERT: G 36 LYS cc_start: 0.9274 (ttmm) cc_final: 0.9030 (ttmm) REVERT: G 64 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8949 (pp20) REVERT: G 104 GLN cc_start: 0.8495 (mp10) cc_final: 0.8178 (mp10) REVERT: H 65 ASP cc_start: 0.9308 (t70) cc_final: 0.9053 (t0) REVERT: H 73 GLU cc_start: 0.9245 (tp30) cc_final: 0.8765 (tp30) REVERT: H 90 GLU cc_start: 0.9279 (pm20) cc_final: 0.8955 (pm20) outliers start: 11 outliers final: 5 residues processed: 139 average time/residue: 0.0936 time to fit residues: 19.7714 Evaluate side-chains 129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.040807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.029504 restraints weight = 137108.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.030159 restraints weight = 65606.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.030543 restraints weight = 41935.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030805 restraints weight = 33012.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030850 restraints weight = 28335.146| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 13264 Z= 0.281 Angle : 0.788 11.929 19238 Z= 0.434 Chirality : 0.046 0.261 2184 Planarity : 0.005 0.050 1361 Dihedral : 32.164 88.410 4224 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.46 % Allowed : 20.47 % Favored : 76.06 % 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: 1.48 (0.29), residues: 746 helix: 1.60 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.74 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 116 TYR 0.050 0.003 TYR F 88 PHE 0.013 0.002 PHE F 100 HIS 0.050 0.004 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.28 (13264) covalent geometry : angle 0.78843 / 0.43 (19238) hydrogen bonds : bond 0.07790 / 5.34 ( 810) hydrogen bonds : angle 3.78208 / 2.79 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9383 (tp30) cc_final: 0.9131 (tp30) REVERT: A 105 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8546 (tm-30) REVERT: B 53 GLU cc_start: 0.8960 (mp0) cc_final: 0.8598 (mp0) REVERT: B 63 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: B 74 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8393 (mt-10) REVERT: B 84 MET cc_start: 0.9303 (mmm) cc_final: 0.8826 (mmm) REVERT: B 88 TYR cc_start: 0.9046 (m-10) cc_final: 0.8470 (m-10) REVERT: C 61 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8542 (mm-30) REVERT: D 65 ASP cc_start: 0.9173 (t0) cc_final: 0.8734 (t0) REVERT: E 65 LEU cc_start: 0.9878 (OUTLIER) cc_final: 0.9565 (mm) REVERT: E 76 GLN cc_start: 0.9173 (mt0) cc_final: 0.8836 (mp10) REVERT: E 97 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8432 (mt-10) REVERT: E 120 MET cc_start: 0.7630 (mpp) cc_final: 0.7251 (mpp) REVERT: F 53 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8981 (mt-10) REVERT: F 63 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8804 (mp0) REVERT: G 64 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8961 (pp20) REVERT: G 104 GLN cc_start: 0.8691 (mp10) cc_final: 0.8384 (mp10) REVERT: H 65 ASP cc_start: 0.9295 (t70) cc_final: 0.9045 (t0) REVERT: H 73 GLU cc_start: 0.9328 (tp30) cc_final: 0.8958 (tp30) REVERT: H 102 GLU cc_start: 0.8893 (tp30) cc_final: 0.8515 (tp30) outliers start: 22 outliers final: 13 residues processed: 129 average time/residue: 0.0897 time to fit residues: 17.9815 Evaluate side-chains 125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 64 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 34 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 31 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.030655 restraints weight = 132681.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.031316 restraints weight = 64685.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.031694 restraints weight = 41251.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031929 restraints weight = 32724.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.032178 restraints weight = 28382.086| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13264 Z= 0.151 Angle : 0.672 11.010 19238 Z= 0.384 Chirality : 0.043 0.252 2184 Planarity : 0.004 0.050 1361 Dihedral : 32.076 89.786 4224 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.89 % Allowed : 22.99 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.30), residues: 746 helix: 1.89 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.76 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.031 0.002 TYR H 80 PHE 0.008 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (13264) covalent geometry : angle 0.67183 / 0.38 (19238) hydrogen bonds : bond 0.04615 / 3.21 ( 810) hydrogen bonds : angle 3.33630 / 2.43 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8489 (tm-30) REVERT: A 120 MET cc_start: 0.8697 (mmm) cc_final: 0.8146 (mmm) REVERT: B 53 GLU cc_start: 0.8966 (mp0) cc_final: 0.8685 (mp0) REVERT: B 63 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: B 74 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 84 MET cc_start: 0.9248 (mmm) cc_final: 0.8745 (mmm) REVERT: B 88 TYR cc_start: 0.9037 (m-10) cc_final: 0.8550 (m-10) REVERT: C 39 TYR cc_start: 0.9559 (m-80) cc_final: 0.9314 (m-80) REVERT: C 56 GLU cc_start: 0.8847 (tt0) cc_final: 0.8424 (mm-30) REVERT: C 61 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8718 (mm-30) REVERT: D 65 ASP cc_start: 0.9091 (t0) cc_final: 0.8639 (t0) REVERT: E 97 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8391 (mt-10) REVERT: E 120 MET cc_start: 0.7770 (mpp) cc_final: 0.7402 (mpp) REVERT: F 53 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8902 (mt-10) REVERT: G 64 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8981 (pp20) REVERT: H 65 ASP cc_start: 0.9300 (t70) cc_final: 0.9049 (t0) REVERT: H 73 GLU cc_start: 0.9295 (tp30) cc_final: 0.8923 (tp30) REVERT: H 102 GLU cc_start: 0.8728 (tp30) cc_final: 0.8288 (tp30) outliers start: 12 outliers final: 6 residues processed: 134 average time/residue: 0.1009 time to fit residues: 20.4361 Evaluate side-chains 123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 40.0000 chunk 82 optimal weight: 30.0000 chunk 69 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 98 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.041354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.030070 restraints weight = 133559.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.030714 restraints weight = 64576.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.031073 restraints weight = 41501.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031303 restraints weight = 33084.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.031554 restraints weight = 28761.308| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13264 Z= 0.186 Angle : 0.705 11.572 19238 Z= 0.397 Chirality : 0.043 0.269 2184 Planarity : 0.004 0.055 1361 Dihedral : 32.036 89.575 4224 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.89 % Allowed : 22.99 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.30), residues: 746 helix: 1.85 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.84 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.015 0.002 TYR F 88 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (13264) covalent geometry : angle 0.70550 / 0.40 (19238) hydrogen bonds : bond 0.04967 / 3.43 ( 810) hydrogen bonds : angle 3.44522 / 2.52 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8542 (tm-30) REVERT: B 53 GLU cc_start: 0.8975 (mp0) cc_final: 0.8701 (mp0) REVERT: B 63 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8631 (mp0) REVERT: B 74 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8265 (mt-10) REVERT: B 84 MET cc_start: 0.9270 (mmm) cc_final: 0.8758 (mmm) REVERT: B 88 TYR cc_start: 0.9031 (m-10) cc_final: 0.8549 (m-10) REVERT: C 39 TYR cc_start: 0.9549 (m-80) cc_final: 0.9309 (m-80) REVERT: C 56 GLU cc_start: 0.8836 (tt0) cc_final: 0.8477 (mm-30) REVERT: C 61 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8721 (mm-30) REVERT: D 65 ASP cc_start: 0.9118 (t0) cc_final: 0.8666 (t0) REVERT: E 65 LEU cc_start: 0.9864 (OUTLIER) cc_final: 0.9570 (mm) REVERT: E 97 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8418 (mt-10) REVERT: E 120 MET cc_start: 0.7823 (mpp) cc_final: 0.7401 (mpp) REVERT: F 53 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8901 (mt-10) REVERT: F 63 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8760 (mp0) REVERT: H 65 ASP cc_start: 0.9289 (t70) cc_final: 0.9037 (t0) REVERT: H 73 GLU cc_start: 0.9303 (tp30) cc_final: 0.8971 (tp30) REVERT: H 80 TYR cc_start: 0.7251 (m-80) cc_final: 0.7007 (m-80) REVERT: H 102 GLU cc_start: 0.8743 (tp30) cc_final: 0.8298 (tp30) outliers start: 12 outliers final: 7 residues processed: 127 average time/residue: 0.1009 time to fit residues: 19.3689 Evaluate side-chains 125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 78 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 67 optimal weight: 0.9990 chunk 92 optimal weight: 30.0000 chunk 11 optimal weight: 0.0050 chunk 34 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.042184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030920 restraints weight = 131391.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.031562 restraints weight = 63305.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.031900 restraints weight = 40653.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032169 restraints weight = 32734.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.032372 restraints weight = 28088.573| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13264 Z= 0.148 Angle : 0.682 10.823 19238 Z= 0.389 Chirality : 0.043 0.249 2184 Planarity : 0.004 0.057 1361 Dihedral : 31.889 90.980 4224 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.89 % Allowed : 22.99 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.30), residues: 746 helix: 1.76 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.84 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.011 0.001 TYR G 39 PHE 0.008 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (13264) covalent geometry : angle 0.68231 / 0.39 (19238) hydrogen bonds : bond 0.04248 / 2.96 ( 810) hydrogen bonds : angle 3.29024 / 2.40 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9246 (tp30) cc_final: 0.9044 (tp30) REVERT: A 105 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8526 (tm-30) REVERT: A 120 MET cc_start: 0.8517 (mmm) cc_final: 0.7974 (mmm) REVERT: B 53 GLU cc_start: 0.8973 (mp0) cc_final: 0.8757 (mp0) REVERT: B 63 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8614 (mp0) REVERT: B 74 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 84 MET cc_start: 0.9251 (mmm) cc_final: 0.8735 (mmm) REVERT: B 88 TYR cc_start: 0.9054 (m-10) cc_final: 0.8651 (m-10) REVERT: C 39 TYR cc_start: 0.9537 (m-80) cc_final: 0.9265 (m-80) REVERT: C 56 GLU cc_start: 0.8782 (tt0) cc_final: 0.8363 (mm-30) REVERT: C 61 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8791 (mm-30) REVERT: D 65 ASP cc_start: 0.9107 (t0) cc_final: 0.8712 (t0) REVERT: E 50 GLU cc_start: 0.9213 (pt0) cc_final: 0.8985 (pp20) REVERT: E 65 LEU cc_start: 0.9842 (OUTLIER) cc_final: 0.9558 (mm) REVERT: E 97 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8388 (mt-10) REVERT: E 120 MET cc_start: 0.7893 (mpp) cc_final: 0.7461 (mpp) REVERT: H 65 ASP cc_start: 0.9295 (t70) cc_final: 0.9049 (t0) REVERT: H 73 GLU cc_start: 0.9267 (tp30) cc_final: 0.8923 (tp30) REVERT: H 102 GLU cc_start: 0.8590 (tp30) cc_final: 0.8260 (tp30) outliers start: 12 outliers final: 6 residues processed: 131 average time/residue: 0.0896 time to fit residues: 18.0536 Evaluate side-chains 124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 30.0000 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.041896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.030618 restraints weight = 133035.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.031284 restraints weight = 63941.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.031610 restraints weight = 40804.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031910 restraints weight = 32984.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.032163 restraints weight = 27727.134| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13264 Z= 0.155 Angle : 0.693 11.123 19238 Z= 0.393 Chirality : 0.043 0.262 2184 Planarity : 0.004 0.058 1361 Dihedral : 31.858 91.133 4224 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.10 % Allowed : 25.04 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.30), residues: 746 helix: 1.72 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.82 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.027 0.002 TYR F 88 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (13264) covalent geometry : angle 0.69340 / 0.39 (19238) hydrogen bonds : bond 0.04381 / 3.04 ( 810) hydrogen bonds : angle 3.35616 / 2.45 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8454 (tm-30) REVERT: A 120 MET cc_start: 0.8540 (mmm) cc_final: 0.8003 (mmm) REVERT: B 53 GLU cc_start: 0.9005 (mp0) cc_final: 0.8772 (mp0) REVERT: B 63 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8668 (mp0) REVERT: B 74 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8223 (mt-10) REVERT: B 84 MET cc_start: 0.9294 (mmm) cc_final: 0.8762 (mmm) REVERT: B 88 TYR cc_start: 0.9069 (m-10) cc_final: 0.8626 (m-10) REVERT: C 39 TYR cc_start: 0.9551 (m-80) cc_final: 0.9321 (m-80) REVERT: C 56 GLU cc_start: 0.8804 (tt0) cc_final: 0.8360 (mm-30) REVERT: C 61 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8767 (mm-30) REVERT: D 65 ASP cc_start: 0.9132 (t0) cc_final: 0.8743 (t0) REVERT: E 50 GLU cc_start: 0.9257 (pt0) cc_final: 0.9014 (pp20) REVERT: E 65 LEU cc_start: 0.9850 (OUTLIER) cc_final: 0.9556 (mm) REVERT: E 97 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8428 (mt-10) REVERT: E 120 MET cc_start: 0.7952 (mpp) cc_final: 0.7493 (mpp) REVERT: H 65 ASP cc_start: 0.9299 (t70) cc_final: 0.9046 (t0) REVERT: H 73 GLU cc_start: 0.9315 (tp30) cc_final: 0.9006 (tp30) REVERT: H 102 GLU cc_start: 0.8670 (tp30) cc_final: 0.8307 (tp30) outliers start: 7 outliers final: 4 residues processed: 120 average time/residue: 0.0902 time to fit residues: 16.6335 Evaluate side-chains 120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.038657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.026628 restraints weight = 116563.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.027235 restraints weight = 57421.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.027616 restraints weight = 36679.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.027837 restraints weight = 28472.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.027972 restraints weight = 24873.440| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13264 Z= 0.149 Angle : 0.692 11.650 19238 Z= 0.391 Chirality : 0.042 0.222 2184 Planarity : 0.004 0.059 1361 Dihedral : 31.819 91.162 4224 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.10 % Allowed : 25.20 % Favored : 73.70 % 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: 1.68 (0.30), residues: 746 helix: 1.78 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.76 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.033 0.002 TYR H 80 PHE 0.008 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (13264) covalent geometry : angle 0.69154 / 0.39 (19238) hydrogen bonds : bond 0.04189 / 2.93 ( 810) hydrogen bonds : angle 3.29448 / 2.41 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2058.95 seconds wall clock time: 36 minutes 11.91 seconds (2171.91 seconds total)