Starting phenix.real_space_refine on Fri Jul 3 04:53:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y00_33536/07_2026/7y00_33536.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y00_33536/07_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_33536/07_2026/7y00_33536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y00_33536/07_2026/7y00_33536.map" model { file = "/net/cci-nas-00/data/ceres_data/7y00_33536/07_2026/7y00_33536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y00_33536/07_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-dev-6108/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: 2.85, per 1000 atoms: 0.23 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: 1.09 Conformation dependent library (CDL) restraints added in 380.1 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: 1.47 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: 2.08 Time building geometry restraints manager: 1.44 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: 18063 1.73 - 3.46: 1113 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: 2.220 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.650 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- 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 : 0.833 8.646 19238 Z= 0.713 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 0.83283 / 0.71 (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 : 0.326 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: 0.0979 time to fit residues: 27.3590 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 : 0.300 ------------------------------------------------------------------------------- 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: 7.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.051279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040253 restraints weight = 130807.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041046 restraints weight = 63033.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.041566 restraints weight = 39707.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.041763 restraints weight = 30029.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.042068 restraints weight = 26477.288| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 13264 Z= 0.196 Angle : 0.680 9.798 19238 Z= 0.406 Chirality : 0.044 0.200 2184 Planarity : 0.005 0.057 1361 Dihedral : 31.111 91.338 4224 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.89 % Allowed : 13.07 % Favored : 85.04 % 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: 1.97 (0.30), residues: 746 helix: 1.92 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.41 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.028 0.002 TYR C 50 PHE 0.008 0.001 PHE A 84 HIS 0.007 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (13264) covalent geometry : angle 0.68006 / 0.41 (19238) hydrogen bonds : bond 0.05638 / 3.87 ( 810) hydrogen bonds : angle 3.35134 / 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 166 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8998 (tt0) cc_final: 0.8279 (tt0) REVERT: A 105 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8596 (tm-30) REVERT: B 49 LEU cc_start: 0.9310 (mt) cc_final: 0.8795 (mt) REVERT: B 53 GLU cc_start: 0.8743 (mp0) cc_final: 0.8383 (mp0) REVERT: B 59 LYS cc_start: 0.9228 (tppp) cc_final: 0.8649 (tppp) REVERT: B 63 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8638 (mp0) REVERT: B 88 TYR cc_start: 0.8913 (m-10) cc_final: 0.8534 (m-10) REVERT: C 90 ASP cc_start: 0.8695 (t0) cc_final: 0.8418 (t70) REVERT: D 65 ASP cc_start: 0.9169 (t0) cc_final: 0.8655 (t0) REVERT: D 68 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8436 (tm-30) REVERT: E 120 MET cc_start: 0.7602 (mtm) cc_final: 0.7113 (mpp) REVERT: F 63 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8657 (mt-10) REVERT: F 93 GLN cc_start: 0.9365 (tp40) cc_final: 0.9080 (tp40) REVERT: G 64 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8647 (tm-30) REVERT: G 104 GLN cc_start: 0.8138 (mp10) cc_final: 0.7800 (mp10) REVERT: H 65 ASP cc_start: 0.9309 (t70) cc_final: 0.9066 (t0) REVERT: H 73 GLU cc_start: 0.9247 (tp30) cc_final: 0.8836 (tp30) REVERT: H 80 TYR cc_start: 0.7795 (m-10) cc_final: 0.7036 (m-10) outliers start: 12 outliers final: 6 residues processed: 160 average time/residue: 0.0913 time to fit residues: 21.9808 Evaluate side-chains 137 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 63 GLU 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: 0.7980 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.050331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.039317 restraints weight = 131386.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040117 restraints weight = 62909.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.040629 restraints weight = 39090.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.040863 restraints weight = 29428.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.041099 restraints weight = 25721.374| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13264 Z= 0.155 Angle : 0.632 7.951 19238 Z= 0.377 Chirality : 0.042 0.182 2184 Planarity : 0.005 0.055 1361 Dihedral : 31.423 92.091 4224 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.52 % Allowed : 15.75 % Favored : 81.73 % 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: 2.09 (0.30), residues: 746 helix: 2.05 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 116 TYR 0.015 0.002 TYR C 50 PHE 0.032 0.002 PHE E 67 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (13264) covalent geometry : angle 0.63231 / 0.38 (19238) hydrogen bonds : bond 0.04615 / 3.19 ( 810) hydrogen bonds : angle 3.17506 / 2.31 ( 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 181 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8982 (tt0) cc_final: 0.8255 (tt0) REVERT: A 97 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8468 (mt-10) REVERT: A 105 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8535 (tm-30) REVERT: B 49 LEU cc_start: 0.9335 (mt) cc_final: 0.8838 (mt) REVERT: B 53 GLU cc_start: 0.8794 (mp0) cc_final: 0.8391 (pm20) REVERT: B 59 LYS cc_start: 0.9116 (tppp) cc_final: 0.8440 (tppp) REVERT: B 63 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: B 88 TYR cc_start: 0.8913 (m-10) cc_final: 0.8464 (m-10) REVERT: C 61 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8430 (mm-30) REVERT: C 90 ASP cc_start: 0.8751 (t0) cc_final: 0.8503 (t70) REVERT: D 65 ASP cc_start: 0.9204 (t0) cc_final: 0.8660 (t0) REVERT: D 68 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8446 (tm-30) REVERT: E 97 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8608 (mt-10) REVERT: F 53 GLU cc_start: 0.9095 (mp0) cc_final: 0.8124 (mp0) REVERT: F 88 TYR cc_start: 0.8511 (m-80) cc_final: 0.8047 (m-10) REVERT: F 93 GLN cc_start: 0.9383 (tp40) cc_final: 0.9157 (tp40) REVERT: G 64 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8815 (tm-30) REVERT: G 104 GLN cc_start: 0.8269 (mp10) cc_final: 0.7962 (mp10) REVERT: H 65 ASP cc_start: 0.9327 (t70) cc_final: 0.9067 (t0) REVERT: H 73 GLU cc_start: 0.9232 (tp30) cc_final: 0.8809 (tp30) REVERT: H 80 TYR cc_start: 0.7656 (m-10) cc_final: 0.6984 (m-10) outliers start: 16 outliers final: 5 residues processed: 172 average time/residue: 0.0921 time to fit residues: 23.7529 Evaluate side-chains 142 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 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: 1.9990 chunk 75 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 31 HIS D 44 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.042961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.031825 restraints weight = 135757.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.032508 restraints weight = 65169.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.032959 restraints weight = 41147.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.033195 restraints weight = 31326.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.033311 restraints weight = 27434.595| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 13264 Z= 0.311 Angle : 0.825 13.944 19238 Z= 0.458 Chirality : 0.048 0.362 2184 Planarity : 0.006 0.053 1361 Dihedral : 32.080 89.744 4224 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.99 % Allowed : 17.64 % Favored : 79.37 % 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: 1.32 (0.29), residues: 746 helix: 1.45 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.68 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 116 TYR 0.020 0.002 TYR G 39 PHE 0.022 0.003 PHE E 67 HIS 0.010 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.31 (13264) covalent geometry : angle 0.82469 / 0.46 (19238) hydrogen bonds : bond 0.08651 / 5.93 ( 810) hydrogen bonds : angle 3.84462 / 2.81 ( 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 156 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8549 (tm-30) REVERT: B 53 GLU cc_start: 0.8949 (mp0) cc_final: 0.8543 (mp0) REVERT: B 63 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: B 84 MET cc_start: 0.9356 (mmm) cc_final: 0.8933 (mmm) REVERT: B 88 TYR cc_start: 0.9062 (m-10) cc_final: 0.8470 (m-10) REVERT: C 39 TYR cc_start: 0.9497 (m-80) cc_final: 0.9175 (m-80) REVERT: C 61 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8562 (mm-30) REVERT: C 90 ASP cc_start: 0.8862 (t0) cc_final: 0.8642 (t70) REVERT: D 65 ASP cc_start: 0.9196 (t0) cc_final: 0.8701 (t0) REVERT: D 68 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8527 (tm-30) REVERT: E 76 GLN cc_start: 0.9149 (mp10) cc_final: 0.8863 (mp10) REVERT: F 53 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8967 (mp0) REVERT: F 63 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8778 (mp0) REVERT: F 84 MET cc_start: 0.9077 (tpp) cc_final: 0.8688 (tpp) REVERT: G 104 GLN cc_start: 0.8614 (mp10) cc_final: 0.8362 (mp10) REVERT: H 65 ASP cc_start: 0.9327 (t70) cc_final: 0.9091 (t0) REVERT: H 73 GLU cc_start: 0.9324 (tp30) cc_final: 0.8906 (tp30) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 0.0862 time to fit residues: 18.9030 Evaluate side-chains 132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 81 VAL 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 124 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 4.9990 chunk 88 optimal weight: 40.0000 chunk 95 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.043806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.032409 restraints weight = 131927.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.033119 restraints weight = 62346.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.033465 restraints weight = 39110.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033783 restraints weight = 31367.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.034045 restraints weight = 26312.115| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 0.046 13264 Z= 0.157 Angle : 0.661 9.466 19238 Z= 0.381 Chirality : 0.043 0.282 2184 Planarity : 0.004 0.050 1361 Dihedral : 32.052 90.811 4224 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.20 % Allowed : 21.26 % Favored : 76.54 % 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 : -0.70 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.017 0.002 TYR H 80 PHE 0.032 0.002 PHE E 67 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (13264) covalent geometry : angle 0.66070 / 0.38 (19238) hydrogen bonds : bond 0.04683 / 3.25 ( 810) hydrogen bonds : angle 3.31546 / 2.42 ( 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 151 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9287 (tp30) cc_final: 0.9041 (tp30) REVERT: A 105 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8516 (tm-30) REVERT: B 53 GLU cc_start: 0.8968 (mp0) cc_final: 0.8530 (mp0) REVERT: B 63 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: B 88 TYR cc_start: 0.9045 (m-10) cc_final: 0.8622 (m-10) REVERT: C 39 TYR cc_start: 0.9494 (m-80) cc_final: 0.9178 (m-80) REVERT: C 90 ASP cc_start: 0.8857 (t0) cc_final: 0.8649 (t70) REVERT: D 65 ASP cc_start: 0.9118 (t0) cc_final: 0.8668 (t0) REVERT: D 68 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8498 (tm-30) REVERT: E 76 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8717 (mp10) REVERT: E 97 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8371 (mt-10) REVERT: F 53 GLU cc_start: 0.9268 (mp0) cc_final: 0.8913 (mp0) REVERT: F 63 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8705 (mp0) REVERT: G 56 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8377 (mm-30) REVERT: G 64 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8909 (pp20) REVERT: G 112 GLN cc_start: 0.9315 (mp10) cc_final: 0.8990 (mp10) REVERT: H 65 ASP cc_start: 0.9295 (t70) cc_final: 0.9028 (t0) REVERT: H 73 GLU cc_start: 0.9300 (tp30) cc_final: 0.8807 (tp30) outliers start: 14 outliers final: 5 residues processed: 141 average time/residue: 0.0827 time to fit residues: 17.9050 Evaluate side-chains 130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 E residue 62 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 64 GLU 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: 2.9990 chunk 81 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 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: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.041194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.029926 restraints weight = 135294.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030583 restraints weight = 64716.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.030996 restraints weight = 41193.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.031173 restraints weight = 31861.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.031286 restraints weight = 28373.735| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 13264 Z= 0.255 Angle : 0.751 10.940 19238 Z= 0.420 Chirality : 0.045 0.249 2184 Planarity : 0.005 0.048 1361 Dihedral : 32.203 90.017 4224 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.31 % Allowed : 20.94 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.29), residues: 746 helix: 1.74 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.82 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 134 TYR 0.026 0.002 TYR F 88 PHE 0.015 0.002 PHE E 67 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.26 (13264) covalent geometry : angle 0.75138 / 0.42 (19238) hydrogen bonds : bond 0.06851 / 4.70 ( 810) hydrogen bonds : angle 3.71904 / 2.71 ( 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 137 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8434 (mt-10) REVERT: A 105 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8579 (tm-30) REVERT: B 53 GLU cc_start: 0.8971 (mp0) cc_final: 0.8698 (mp0) REVERT: B 63 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: B 88 TYR cc_start: 0.9078 (m-10) cc_final: 0.8624 (m-10) REVERT: C 90 ASP cc_start: 0.8992 (t0) cc_final: 0.8776 (t0) REVERT: D 65 ASP cc_start: 0.9198 (t0) cc_final: 0.8753 (t0) REVERT: D 68 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8603 (tm-30) REVERT: E 76 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8749 (mp10) REVERT: E 97 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8400 (mt-10) REVERT: E 120 MET cc_start: 0.7732 (mpp) cc_final: 0.7460 (mpp) REVERT: F 53 GLU cc_start: 0.9292 (mp0) cc_final: 0.8774 (mp0) REVERT: F 88 TYR cc_start: 0.8964 (m-80) cc_final: 0.8260 (m-10) REVERT: G 64 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.9011 (pp20) REVERT: H 65 ASP cc_start: 0.9314 (t70) cc_final: 0.9048 (t0) REVERT: H 73 GLU cc_start: 0.9328 (tp30) cc_final: 0.9046 (tp30) REVERT: H 102 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8599 (tp30) REVERT: H 103 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9418 (mp) outliers start: 21 outliers final: 9 residues processed: 131 average time/residue: 0.0774 time to fit residues: 15.9191 Evaluate side-chains 124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 E residue 62 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 89 VAL 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 H residue 49 THR Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 7 optimal weight: 0.0060 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.041908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.030559 restraints weight = 133089.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.031233 restraints weight = 64576.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031565 restraints weight = 40925.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031862 restraints weight = 33027.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032016 restraints weight = 27969.309| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13264 Z= 0.162 Angle : 0.664 9.377 19238 Z= 0.383 Chirality : 0.043 0.252 2184 Planarity : 0.004 0.058 1361 Dihedral : 32.158 90.830 4224 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.73 % Allowed : 22.83 % Favored : 75.43 % 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: 1.87 (0.30), residues: 746 helix: 1.95 (0.21), residues: 550 sheet: None (None), residues: 0 loop : -0.81 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.046 0.002 TYR F 88 PHE 0.013 0.001 PHE E 67 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (13264) covalent geometry : angle 0.66408 / 0.38 (19238) hydrogen bonds : bond 0.04575 / 3.17 ( 810) hydrogen bonds : angle 3.37780 / 2.47 ( 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 139 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 105 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8517 (tm-30) REVERT: A 120 MET cc_start: 0.8633 (mmm) cc_final: 0.8085 (mmm) REVERT: B 53 GLU cc_start: 0.8983 (mp0) cc_final: 0.8541 (mp0) REVERT: B 63 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: B 84 MET cc_start: 0.9291 (mmm) cc_final: 0.8828 (mmm) REVERT: B 88 TYR cc_start: 0.9033 (m-10) cc_final: 0.8547 (m-10) REVERT: D 65 ASP cc_start: 0.9079 (t0) cc_final: 0.8642 (t0) REVERT: D 68 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8601 (tm-30) REVERT: E 50 GLU cc_start: 0.9393 (pt0) cc_final: 0.9188 (pt0) REVERT: E 97 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8353 (mt-10) REVERT: E 120 MET cc_start: 0.7764 (mpp) cc_final: 0.7503 (mpp) REVERT: F 53 GLU cc_start: 0.9252 (mp0) cc_final: 0.8747 (mp0) REVERT: F 63 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8688 (mp0) REVERT: F 88 TYR cc_start: 0.8809 (m-80) cc_final: 0.8495 (m-10) REVERT: G 56 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8482 (mm-30) REVERT: G 64 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8969 (pp20) REVERT: H 65 ASP cc_start: 0.9302 (t70) cc_final: 0.9049 (t0) REVERT: H 73 GLU cc_start: 0.9286 (tp30) cc_final: 0.8909 (tp30) REVERT: H 102 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8635 (tp30) outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.0814 time to fit residues: 16.4505 Evaluate side-chains 121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 78 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 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: 5.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.041159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.029847 restraints weight = 133842.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030499 restraints weight = 64587.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030830 restraints weight = 41204.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.031089 restraints weight = 33219.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031301 restraints weight = 28350.984| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 : 0.004 0.058 13264 Z= 0.191 Angle : 0.700 12.051 19238 Z= 0.398 Chirality : 0.043 0.250 2184 Planarity : 0.004 0.058 1361 Dihedral : 32.133 90.965 4224 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.89 % Allowed : 23.94 % Favored : 74.17 % 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 : -0.85 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.044 0.002 TYR F 88 PHE 0.009 0.002 PHE E 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.19 (13264) covalent geometry : angle 0.70032 / 0.40 (19238) hydrogen bonds : bond 0.05128 / 3.54 ( 810) hydrogen bonds : angle 3.48275 / 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 131 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8392 (mt-10) REVERT: A 105 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8600 (tm-30) REVERT: B 53 GLU cc_start: 0.8992 (mp0) cc_final: 0.8712 (mp0) REVERT: B 63 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: B 84 MET cc_start: 0.9313 (mmm) cc_final: 0.8845 (mmm) REVERT: B 88 TYR cc_start: 0.9045 (m-10) cc_final: 0.8564 (m-10) REVERT: D 65 ASP cc_start: 0.9122 (t0) cc_final: 0.8690 (t0) REVERT: D 68 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8664 (tm-30) REVERT: E 65 LEU cc_start: 0.9866 (OUTLIER) cc_final: 0.9583 (mm) REVERT: E 97 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8394 (mt-10) REVERT: E 120 MET cc_start: 0.7856 (mpp) cc_final: 0.7483 (mpp) REVERT: F 53 GLU cc_start: 0.9261 (mp0) cc_final: 0.8756 (mp0) REVERT: F 88 TYR cc_start: 0.8554 (m-80) cc_final: 0.8222 (m-10) REVERT: G 56 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8477 (mm-30) REVERT: G 64 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9031 (pp20) REVERT: H 65 ASP cc_start: 0.9293 (t70) cc_final: 0.9040 (t0) REVERT: H 73 GLU cc_start: 0.9329 (tp30) cc_final: 0.8987 (tp30) REVERT: H 102 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8561 (tp30) outliers start: 12 outliers final: 8 residues processed: 126 average time/residue: 0.0938 time to fit residues: 17.9153 Evaluate side-chains 122 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 G residue 78 ILE Chi-restraints excluded: chain H residue 49 THR 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: 0.9990 chunk 88 optimal weight: 50.0000 chunk 67 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.0070 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.038703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.026241 restraints weight = 117374.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.026805 restraints weight = 58487.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.027174 restraints weight = 38407.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.027383 restraints weight = 30225.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.027516 restraints weight = 26589.171| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13264 Z= 0.152 Angle : 0.682 10.666 19238 Z= 0.390 Chirality : 0.043 0.277 2184 Planarity : 0.004 0.061 1361 Dihedral : 32.027 92.305 4224 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.89 % Allowed : 24.25 % 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: 1.67 (0.30), residues: 746 helix: 1.79 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 39 TYR 0.049 0.002 TYR F 88 PHE 0.010 0.001 PHE G 25 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (13264) covalent geometry : angle 0.68239 / 0.39 (19238) hydrogen bonds : bond 0.04309 / 2.98 ( 810) hydrogen bonds : angle 3.34112 / 2.41 ( 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 138 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8352 (mt-10) REVERT: A 105 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 120 MET cc_start: 0.8555 (mmm) cc_final: 0.8007 (mmm) REVERT: B 53 GLU cc_start: 0.8999 (mp0) cc_final: 0.8744 (mp0) REVERT: B 59 LYS cc_start: 0.9192 (tppp) cc_final: 0.8705 (tppt) REVERT: B 63 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: B 84 MET cc_start: 0.9275 (mmm) cc_final: 0.8793 (mmm) REVERT: B 88 TYR cc_start: 0.9050 (m-10) cc_final: 0.8613 (m-10) REVERT: D 65 ASP cc_start: 0.9135 (t0) cc_final: 0.8749 (t0) REVERT: D 68 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8625 (tm-30) REVERT: E 65 LEU cc_start: 0.9849 (OUTLIER) cc_final: 0.9562 (mm) REVERT: E 97 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8405 (mt-10) REVERT: E 120 MET cc_start: 0.7839 (mpp) cc_final: 0.7492 (mpp) REVERT: F 53 GLU cc_start: 0.9235 (mp0) cc_final: 0.8724 (mp0) REVERT: F 63 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8704 (mp0) REVERT: G 56 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8488 (mm-30) REVERT: G 64 GLU cc_start: 0.9298 (tm-30) cc_final: 0.9003 (pp20) REVERT: H 65 ASP cc_start: 0.9302 (t70) cc_final: 0.9050 (t0) REVERT: H 73 GLU cc_start: 0.9282 (tp30) cc_final: 0.8902 (tp30) outliers start: 12 outliers final: 7 residues processed: 135 average time/residue: 0.0870 time to fit residues: 17.8786 Evaluate side-chains 128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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: 20.0000 chunk 65 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 23 optimal weight: 0.1980 chunk 73 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 86 optimal weight: 50.0000 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.041688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.030495 restraints weight = 132405.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.031140 restraints weight = 63690.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.031471 restraints weight = 40761.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031764 restraints weight = 32745.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031989 restraints weight = 27868.271| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13264 Z= 0.155 Angle : 0.676 9.516 19238 Z= 0.387 Chirality : 0.042 0.234 2184 Planarity : 0.004 0.061 1361 Dihedral : 31.957 92.644 4224 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.73 % Allowed : 24.72 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.30), residues: 746 helix: 1.76 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.89 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.019 0.001 TYR H 80 PHE 0.062 0.002 PHE E 67 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (13264) covalent geometry : angle 0.67647 / 0.39 (19238) hydrogen bonds : bond 0.04404 / 3.05 ( 810) hydrogen bonds : angle 3.34580 / 2.40 ( 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 133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8386 (mt-10) REVERT: A 105 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8521 (tm-30) REVERT: B 53 GLU cc_start: 0.9006 (mp0) cc_final: 0.8649 (mp0) REVERT: B 59 LYS cc_start: 0.9168 (tppp) cc_final: 0.8705 (ttmm) REVERT: B 63 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: B 84 MET cc_start: 0.9291 (mmm) cc_final: 0.8815 (mmm) REVERT: B 88 TYR cc_start: 0.9027 (m-10) cc_final: 0.8587 (m-10) REVERT: D 65 ASP cc_start: 0.9123 (t0) cc_final: 0.8754 (t0) REVERT: D 68 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8595 (tm-30) REVERT: E 65 LEU cc_start: 0.9843 (OUTLIER) cc_final: 0.9560 (mm) REVERT: E 97 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8346 (mt-10) REVERT: E 120 MET cc_start: 0.7833 (mpp) cc_final: 0.7482 (mpp) REVERT: F 53 GLU cc_start: 0.9236 (mp0) cc_final: 0.8733 (mp0) REVERT: F 63 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8685 (mp0) REVERT: G 56 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8478 (mm-30) REVERT: G 64 GLU cc_start: 0.9283 (tm-30) cc_final: 0.8997 (pp20) REVERT: H 65 ASP cc_start: 0.9288 (t70) cc_final: 0.9036 (t0) REVERT: H 73 GLU cc_start: 0.9289 (tp30) cc_final: 0.8983 (tp30) outliers start: 11 outliers final: 9 residues processed: 129 average time/residue: 0.0796 time to fit residues: 15.7075 Evaluate side-chains 128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 30 VAL 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 F residue 85 ASP 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 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.041916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030695 restraints weight = 130997.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.031341 restraints weight = 62895.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.031690 restraints weight = 40139.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031985 restraints weight = 32036.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032052 restraints weight = 27436.470| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.5357 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= 0.152 Angle : 0.683 12.071 19238 Z= 0.390 Chirality : 0.042 0.219 2184 Planarity : 0.004 0.062 1361 Dihedral : 31.909 93.029 4224 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.73 % Allowed : 25.83 % Favored : 72.44 % 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: 1.52 (0.30), residues: 746 helix: 1.67 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.057 0.002 TYR F 88 PHE 0.012 0.001 PHE E 67 HIS 0.009 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (13264) covalent geometry : angle 0.68250 / 0.39 (19238) hydrogen bonds : bond 0.04241 / 2.93 ( 810) hydrogen bonds : angle 3.34833 / 2.41 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.27 seconds wall clock time: 32 minutes 18.28 seconds (1938.28 seconds total)