Starting phenix.real_space_refine on Fri Jul 3 15:35:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pew_13359/07_2026/7pew_13359.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pew_13359/07_2026/7pew_13359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pew_13359/07_2026/7pew_13359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pew_13359/07_2026/7pew_13359.map" model { file = "/net/cci-nas-00/data/ceres_data/7pew_13359/07_2026/7pew_13359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pew_13359/07_2026/7pew_13359.cif" } resolution = 4.6 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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 352 5.49 5 S 10 5.16 5 C 7254 2.51 5 N 2504 2.21 5 O 3184 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: 13304 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3636 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "I" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3580 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Time building chain proxies: 2.50, per 1000 atoms: 0.19 Number of scatterers: 13304 At special positions: 0 Unit cell: (131.25, 163.8, 117.6, 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 10 16.00 P 352 15.00 O 3184 8.00 N 2504 7.00 C 7254 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: 1.02 Conformation dependent library (CDL) restraints added in 377.2 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 71.9% alpha, 2.6% beta 173 base pairs and 310 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.690A 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 132 removed outlier: 3.623A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.583A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.119A 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: 4.291A 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 'D' and resid 37 through 49 removed outlier: 3.500A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.664A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.254A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (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 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.216A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.641A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.733A 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 removed outlier: 6.602A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.917A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.228A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.026A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 407 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 448 hydrogen bonds 896 hydrogen bond angles 0 basepair planarities 173 basepair parallelities 310 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2350 1.33 - 1.46: 5344 1.46 - 1.58: 5846 1.58 - 1.70: 702 1.70 - 1.83: 20 Bond restraints: 14262 Sorted by residual: bond pdb=" C3' DC I 12 " pdb=" O3' DC I 12 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.56e+01 bond pdb=" C3' DT J 671 " pdb=" C2' DT J 671 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.47e+01 bond pdb=" C5' DC I 168 " pdb=" C4' DC I 168 " ideal model delta sigma weight residual 1.512 1.538 -0.026 7.00e-03 2.04e+04 1.43e+01 bond pdb=" C3' DG I 140 " pdb=" O3' DG I 140 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.30e-02 5.92e+03 1.31e+01 bond pdb=" C3' DC I 123 " pdb=" O3' DC I 123 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.10e+01 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 19677 2.20 - 4.41: 994 4.41 - 6.61: 75 6.61 - 8.81: 22 8.81 - 11.01: 6 Bond angle restraints: 20774 Sorted by residual: angle pdb=" O4' DG I 112 " pdb=" C4' DG I 112 " pdb=" C3' DG I 112 " ideal model delta sigma weight residual 106.00 102.06 3.94 6.00e-01 2.78e+00 4.32e+01 angle pdb=" O4' DC I 92 " pdb=" C4' DC I 92 " pdb=" C3' DC I 92 " ideal model delta sigma weight residual 106.00 102.24 3.76 6.00e-01 2.78e+00 3.94e+01 angle pdb=" N GLU D 113 " pdb=" CA GLU D 113 " pdb=" CB GLU D 113 " ideal model delta sigma weight residual 110.28 118.47 -8.19 1.55e+00 4.16e-01 2.79e+01 angle pdb=" N GLU A 105 " pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " ideal model delta sigma weight residual 110.28 118.46 -8.18 1.55e+00 4.16e-01 2.79e+01 angle pdb=" O4' DA I 153 " pdb=" C4' DA I 153 " pdb=" C3' DA I 153 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.41e+01 ... (remaining 20769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 5814 35.97 - 71.94: 1791 71.94 - 107.90: 26 107.90 - 143.87: 2 143.87 - 179.84: 3 Dihedral angle restraints: 7636 sinusoidal: 5414 harmonic: 2222 Sorted by residual: dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ARG H 33 " pdb=" C ARG H 33 " pdb=" N LYS H 34 " pdb=" CA LYS H 34 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLU E 59 " pdb=" C GLU E 59 " pdb=" N LEU E 60 " pdb=" CA LEU E 60 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 7633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1642 0.050 - 0.100: 559 0.100 - 0.150: 129 0.150 - 0.200: 24 0.200 - 0.251: 6 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CB THR B 54 " pdb=" CA THR B 54 " pdb=" OG1 THR B 54 " pdb=" CG2 THR B 54 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLU A 94 " pdb=" N GLU A 94 " pdb=" C GLU A 94 " pdb=" CB GLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C3' DG I 140 " pdb=" C4' DG I 140 " pdb=" O3' DG I 140 " pdb=" C2' DG I 140 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2357 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 60 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ALA G 60 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA G 60 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU G 61 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 113 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" CD GLU D 113 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU D 113 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU D 113 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 106 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" CG ASP E 106 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP E 106 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP E 106 " -0.013 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2643 2.78 - 3.31: 12088 3.31 - 3.84: 29169 3.84 - 4.37: 32242 4.37 - 4.90: 44010 Nonbonded interactions: 120152 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.249 3.120 nonbonded pdb=" O LYS H 116 " pdb=" OG1 THR H 119 " model vdw 2.274 3.040 nonbonded pdb=" O GLN A 93 " pdb=" OG SER A 96 " model vdw 2.279 3.040 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.282 3.120 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.291 3.040 ... (remaining 120147 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.810 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.007 0.058 14262 Z= 0.625 Angle : 1.041 11.014 20774 Z= 0.813 Chirality : 0.054 0.251 2360 Planarity : 0.007 0.075 1408 Dihedral : 30.189 179.839 6204 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.20 (0.27), residues: 752 helix: 0.18 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 92 TYR 0.035 0.003 TYR D 37 PHE 0.024 0.003 PHE G 25 HIS 0.009 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.62 (14262) covalent geometry : angle 1.04110 / 0.81 (20774) hydrogen bonds : bond 0.11094 / 7.44 ( 855) hydrogen bonds : angle 4.80549 / 3.46 ( 2102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9384 (mpp) cc_final: 0.8851 (mpp) REVERT: A 104 PHE cc_start: 0.9170 (m-80) cc_final: 0.8786 (m-80) REVERT: A 105 GLU cc_start: 0.9474 (pm20) cc_final: 0.9228 (pm20) REVERT: A 106 ASP cc_start: 0.9444 (m-30) cc_final: 0.9074 (m-30) REVERT: A 120 MET cc_start: 0.8366 (mtt) cc_final: 0.8082 (mpp) REVERT: B 59 LYS cc_start: 0.9594 (tmtt) cc_final: 0.9373 (tptt) REVERT: C 25 PHE cc_start: 0.8185 (m-10) cc_final: 0.7745 (m-10) REVERT: D 34 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7645 (tmmt) REVERT: E 50 GLU cc_start: 0.9493 (mp0) cc_final: 0.8859 (pm20) REVERT: E 51 ILE cc_start: 0.9570 (mt) cc_final: 0.9256 (mt) REVERT: E 54 TYR cc_start: 0.9506 (m-80) cc_final: 0.9088 (m-80) REVERT: E 59 GLU cc_start: 0.9093 (mp0) cc_final: 0.8764 (pm20) REVERT: E 90 MET cc_start: 0.9429 (mmp) cc_final: 0.9145 (mmm) REVERT: E 93 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8049 (tm-30) REVERT: E 94 GLU cc_start: 0.9403 (tp30) cc_final: 0.9097 (tp30) REVERT: E 104 PHE cc_start: 0.9622 (m-10) cc_final: 0.9332 (m-80) REVERT: E 105 GLU cc_start: 0.9401 (pp20) cc_final: 0.9194 (pp20) REVERT: E 120 MET cc_start: 0.8744 (mtm) cc_final: 0.8271 (mtt) REVERT: E 123 ASP cc_start: 0.9563 (m-30) cc_final: 0.9310 (m-30) REVERT: F 24 ASP cc_start: 0.9237 (t0) cc_final: 0.9013 (t0) REVERT: F 59 LYS cc_start: 0.9663 (tttp) cc_final: 0.9225 (tppp) REVERT: F 60 VAL cc_start: 0.9651 (t) cc_final: 0.9438 (p) REVERT: F 62 LEU cc_start: 0.9793 (mt) cc_final: 0.9407 (pp) REVERT: F 63 GLU cc_start: 0.9680 (mt-10) cc_final: 0.9299 (mt-10) REVERT: F 85 ASP cc_start: 0.8345 (m-30) cc_final: 0.8126 (m-30) REVERT: G 102 ILE cc_start: 0.8328 (mm) cc_final: 0.8101 (mm) REVERT: H 47 GLN cc_start: 0.9202 (mp10) cc_final: 0.8942 (mp10) REVERT: H 105 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8308 (tm-30) REVERT: H 109 HIS cc_start: 0.9391 (m90) cc_final: 0.8442 (m90) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1024 time to fit residues: 25.5039 Evaluate side-chains 120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN D 109 HIS E 55 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS H 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.020957 restraints weight = 173341.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.021720 restraints weight = 85416.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.022240 restraints weight = 51812.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.022603 restraints weight = 35619.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.022874 restraints weight = 26830.639| |-----------------------------------------------------------------------------| r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14262 Z= 0.205 Angle : 0.740 9.180 20774 Z= 0.428 Chirality : 0.048 0.251 2360 Planarity : 0.005 0.050 1408 Dihedral : 33.513 179.343 4680 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.47 % Allowed : 5.35 % Favored : 94.18 % 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: 1.01 (0.29), residues: 752 helix: 1.10 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 42 TYR 0.016 0.002 TYR B 88 PHE 0.018 0.002 PHE E 67 HIS 0.014 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.20 (14262) covalent geometry : angle 0.73955 / 0.43 (20774) hydrogen bonds : bond 0.06451 / 4.38 ( 855) hydrogen bonds : angle 3.72765 / 2.65 ( 2102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9355 (mpp) cc_final: 0.8895 (mpp) REVERT: A 104 PHE cc_start: 0.9400 (m-80) cc_final: 0.8982 (m-80) REVERT: A 106 ASP cc_start: 0.9377 (m-30) cc_final: 0.9102 (m-30) REVERT: A 120 MET cc_start: 0.8454 (mtt) cc_final: 0.7844 (mpp) REVERT: B 59 LYS cc_start: 0.9641 (tmtt) cc_final: 0.9404 (tptt) REVERT: D 34 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7816 (tmmt) REVERT: D 109 HIS cc_start: 0.9419 (m90) cc_final: 0.8926 (m90) REVERT: E 50 GLU cc_start: 0.9487 (mp0) cc_final: 0.9211 (mp0) REVERT: E 59 GLU cc_start: 0.9083 (mp0) cc_final: 0.8781 (pm20) REVERT: E 90 MET cc_start: 0.9496 (mmp) cc_final: 0.9208 (mmp) REVERT: E 93 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8463 (tm-30) REVERT: E 104 PHE cc_start: 0.9627 (m-10) cc_final: 0.9360 (m-10) REVERT: E 120 MET cc_start: 0.8756 (mtm) cc_final: 0.8111 (mtt) REVERT: E 123 ASP cc_start: 0.9487 (m-30) cc_final: 0.8790 (m-30) REVERT: F 59 LYS cc_start: 0.9648 (tttp) cc_final: 0.9426 (tppp) REVERT: F 60 VAL cc_start: 0.9654 (t) cc_final: 0.9187 (t) REVERT: F 63 GLU cc_start: 0.9701 (mt-10) cc_final: 0.9473 (mt-10) REVERT: F 74 GLU cc_start: 0.9250 (pp20) cc_final: 0.8974 (pp20) REVERT: G 68 ASN cc_start: 0.8997 (p0) cc_final: 0.8713 (p0) REVERT: G 102 ILE cc_start: 0.8424 (mm) cc_final: 0.8219 (mm) REVERT: H 108 LYS cc_start: 0.9330 (ptpp) cc_final: 0.9102 (ptpp) outliers start: 3 outliers final: 3 residues processed: 151 average time/residue: 0.1111 time to fit residues: 24.0308 Evaluate side-chains 114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.027356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.020116 restraints weight = 180566.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.020863 restraints weight = 87476.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.021373 restraints weight = 52699.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.021731 restraints weight = 36148.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.021975 restraints weight = 27130.770| |-----------------------------------------------------------------------------| r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14262 Z= 0.251 Angle : 0.733 11.200 20774 Z= 0.426 Chirality : 0.047 0.269 2360 Planarity : 0.005 0.057 1408 Dihedral : 33.498 179.120 4680 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.79 % Allowed : 4.09 % Favored : 95.13 % 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: 1.14 (0.29), residues: 752 helix: 1.18 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.11 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 92 TYR 0.015 0.002 TYR C 57 PHE 0.026 0.002 PHE C 25 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.25 (14262) covalent geometry : angle 0.73299 / 0.43 (20774) hydrogen bonds : bond 0.08063 / 5.43 ( 855) hydrogen bonds : angle 3.76391 / 2.67 ( 2102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9383 (mpp) cc_final: 0.9060 (mpp) REVERT: A 104 PHE cc_start: 0.9482 (m-80) cc_final: 0.9120 (m-80) REVERT: A 120 MET cc_start: 0.8325 (mtt) cc_final: 0.7161 (mpp) REVERT: B 74 GLU cc_start: 0.9680 (tm-30) cc_final: 0.9434 (tm-30) REVERT: C 50 TYR cc_start: 0.9140 (t80) cc_final: 0.8869 (t80) REVERT: D 34 LYS cc_start: 0.8425 (mmmm) cc_final: 0.7738 (tmmt) REVERT: D 109 HIS cc_start: 0.9318 (m90) cc_final: 0.8921 (m90) REVERT: E 50 GLU cc_start: 0.9567 (mp0) cc_final: 0.9316 (mp0) REVERT: E 59 GLU cc_start: 0.9087 (mp0) cc_final: 0.8669 (pm20) REVERT: E 90 MET cc_start: 0.9445 (mmp) cc_final: 0.9219 (mmp) REVERT: E 93 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8357 (tm-30) REVERT: E 94 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8399 (tp30) REVERT: E 97 GLU cc_start: 0.9266 (pt0) cc_final: 0.8434 (pp20) REVERT: E 104 PHE cc_start: 0.9550 (m-10) cc_final: 0.9270 (m-10) REVERT: E 120 MET cc_start: 0.8648 (mtm) cc_final: 0.7843 (mtt) REVERT: E 123 ASP cc_start: 0.9235 (m-30) cc_final: 0.8595 (m-30) REVERT: F 60 VAL cc_start: 0.9662 (t) cc_final: 0.9191 (t) REVERT: F 63 GLU cc_start: 0.9742 (mt-10) cc_final: 0.9499 (mt-10) REVERT: F 74 GLU cc_start: 0.9270 (pp20) cc_final: 0.9013 (pp20) REVERT: G 61 GLU cc_start: 0.9241 (pp20) cc_final: 0.9036 (pp20) REVERT: G 64 GLU cc_start: 0.9194 (mp0) cc_final: 0.8965 (mp0) REVERT: G 72 ASP cc_start: 0.9328 (m-30) cc_final: 0.9077 (m-30) REVERT: G 102 ILE cc_start: 0.8482 (mm) cc_final: 0.8249 (mm) REVERT: H 59 MET cc_start: 0.7827 (tpt) cc_final: 0.7366 (tmm) REVERT: H 120 LYS cc_start: 0.9649 (mppt) cc_final: 0.9270 (mtmm) outliers start: 5 outliers final: 4 residues processed: 142 average time/residue: 0.1179 time to fit residues: 24.2169 Evaluate side-chains 114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 56 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 104 GLN ** F 25 ASN ** 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 = 0.2831 r_free = 0.2831 target = 0.027862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.020566 restraints weight = 175357.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.021344 restraints weight = 83760.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.021861 restraints weight = 49968.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.022223 restraints weight = 34262.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.022482 restraints weight = 25580.862| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14262 Z= 0.177 Angle : 0.680 8.459 20774 Z= 0.398 Chirality : 0.045 0.285 2360 Planarity : 0.004 0.056 1408 Dihedral : 33.408 179.307 4680 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.16 % Allowed : 2.20 % Favored : 97.64 % 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: 1.28 (0.29), residues: 752 helix: 1.32 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 20 TYR 0.011 0.001 TYR C 57 PHE 0.015 0.002 PHE C 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.18 (14262) covalent geometry : angle 0.67976 / 0.40 (20774) hydrogen bonds : bond 0.05617 / 3.77 ( 855) hydrogen bonds : angle 3.61537 / 2.57 ( 2102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9388 (mpp) cc_final: 0.9128 (mmm) REVERT: A 93 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8939 (tp40) REVERT: A 104 PHE cc_start: 0.9483 (m-80) cc_final: 0.9104 (m-80) REVERT: A 106 ASP cc_start: 0.9451 (m-30) cc_final: 0.9242 (m-30) REVERT: A 120 MET cc_start: 0.8238 (mtt) cc_final: 0.7987 (mtt) REVERT: B 74 GLU cc_start: 0.9689 (tm-30) cc_final: 0.9407 (tm-30) REVERT: C 50 TYR cc_start: 0.9100 (t80) cc_final: 0.8697 (t80) REVERT: D 34 LYS cc_start: 0.8334 (mmmm) cc_final: 0.7664 (tmmt) REVERT: E 50 GLU cc_start: 0.9540 (mp0) cc_final: 0.9280 (mp0) REVERT: E 51 ILE cc_start: 0.9703 (mt) cc_final: 0.9502 (mt) REVERT: E 59 GLU cc_start: 0.9076 (mp0) cc_final: 0.8613 (pm20) REVERT: E 90 MET cc_start: 0.9409 (mmp) cc_final: 0.9200 (mmp) REVERT: E 93 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8406 (tm-30) REVERT: E 94 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8483 (tp30) REVERT: E 97 GLU cc_start: 0.9223 (pt0) cc_final: 0.8517 (pp20) REVERT: E 105 GLU cc_start: 0.9251 (pp20) cc_final: 0.8980 (pp20) REVERT: E 106 ASP cc_start: 0.8742 (m-30) cc_final: 0.8299 (m-30) REVERT: E 120 MET cc_start: 0.8573 (mtm) cc_final: 0.7776 (mtt) REVERT: E 123 ASP cc_start: 0.9173 (m-30) cc_final: 0.8637 (m-30) REVERT: F 60 VAL cc_start: 0.9663 (t) cc_final: 0.9163 (t) REVERT: F 62 LEU cc_start: 0.9804 (mt) cc_final: 0.9437 (pp) REVERT: F 63 GLU cc_start: 0.9723 (mt-10) cc_final: 0.9334 (mt-10) REVERT: F 74 GLU cc_start: 0.9257 (pp20) cc_final: 0.8985 (pp20) REVERT: F 79 LYS cc_start: 0.9480 (tptp) cc_final: 0.9153 (tttt) REVERT: G 64 GLU cc_start: 0.9194 (mp0) cc_final: 0.8959 (mp0) REVERT: G 102 ILE cc_start: 0.8465 (mm) cc_final: 0.8198 (mm) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.1076 time to fit residues: 23.8004 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 87 optimal weight: 30.0000 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 105 optimal weight: 40.0000 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.027744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.020498 restraints weight = 176207.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.021261 restraints weight = 84630.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.021789 restraints weight = 50603.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.022154 restraints weight = 34452.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.022411 restraints weight = 25693.932| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14262 Z= 0.176 Angle : 0.677 8.411 20774 Z= 0.394 Chirality : 0.045 0.284 2360 Planarity : 0.005 0.066 1408 Dihedral : 33.245 179.046 4680 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.31 % Allowed : 2.67 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.29), residues: 752 helix: 1.44 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 42 TYR 0.014 0.001 TYR A 99 PHE 0.011 0.002 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.18 (14262) covalent geometry : angle 0.67696 / 0.39 (20774) hydrogen bonds : bond 0.05569 / 3.73 ( 855) hydrogen bonds : angle 3.51508 / 2.50 ( 2102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9376 (mpp) cc_final: 0.9059 (mpp) REVERT: A 104 PHE cc_start: 0.9508 (m-80) cc_final: 0.9132 (m-80) REVERT: A 120 MET cc_start: 0.8181 (mtt) cc_final: 0.7921 (mtt) REVERT: B 74 GLU cc_start: 0.9698 (tm-30) cc_final: 0.9417 (tm-30) REVERT: C 50 TYR cc_start: 0.9120 (t80) cc_final: 0.8659 (t80) REVERT: D 34 LYS cc_start: 0.8311 (mmmm) cc_final: 0.7616 (tmmt) REVERT: D 109 HIS cc_start: 0.9418 (m170) cc_final: 0.8744 (m90) REVERT: E 50 GLU cc_start: 0.9529 (mp0) cc_final: 0.9288 (pt0) REVERT: E 59 GLU cc_start: 0.9057 (mp0) cc_final: 0.8671 (pm20) REVERT: E 90 MET cc_start: 0.9426 (mmp) cc_final: 0.9219 (mmp) REVERT: E 93 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8501 (tm-30) REVERT: E 94 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8513 (tp30) REVERT: E 97 GLU cc_start: 0.9256 (pt0) cc_final: 0.8575 (pp20) REVERT: E 120 MET cc_start: 0.8568 (mtm) cc_final: 0.7825 (mtt) REVERT: F 60 VAL cc_start: 0.9654 (t) cc_final: 0.9139 (t) REVERT: F 62 LEU cc_start: 0.9809 (mt) cc_final: 0.9452 (pp) REVERT: F 63 GLU cc_start: 0.9706 (mt-10) cc_final: 0.9323 (mt-10) REVERT: F 74 GLU cc_start: 0.9266 (pp20) cc_final: 0.9005 (pp20) REVERT: F 79 LYS cc_start: 0.9519 (tptp) cc_final: 0.9191 (tttt) REVERT: G 61 GLU cc_start: 0.9180 (pp20) cc_final: 0.8747 (pp20) REVERT: G 102 ILE cc_start: 0.8491 (mm) cc_final: 0.8213 (mm) outliers start: 2 outliers final: 1 residues processed: 146 average time/residue: 0.1055 time to fit residues: 22.6306 Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 72 optimal weight: 50.0000 chunk 45 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.021077 restraints weight = 172068.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.021881 restraints weight = 82490.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.022426 restraints weight = 49091.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.022788 restraints weight = 33392.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.023059 restraints weight = 25076.974| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14262 Z= 0.142 Angle : 0.657 8.161 20774 Z= 0.384 Chirality : 0.045 0.292 2360 Planarity : 0.004 0.066 1408 Dihedral : 33.092 179.158 4680 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.31 % Allowed : 2.20 % Favored : 97.48 % 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: 1.41 (0.29), residues: 752 helix: 1.48 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.34 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.015 0.001 TYR D 121 PHE 0.033 0.002 PHE E 104 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.14 (14262) covalent geometry : angle 0.65740 / 0.38 (20774) hydrogen bonds : bond 0.04379 / 2.94 ( 855) hydrogen bonds : angle 3.40475 / 2.42 ( 2102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9439 (tp) cc_final: 0.9196 (tp) REVERT: A 90 MET cc_start: 0.9351 (mpp) cc_final: 0.9113 (mpp) REVERT: A 104 PHE cc_start: 0.9482 (m-80) cc_final: 0.9094 (m-80) REVERT: A 120 MET cc_start: 0.8149 (mtt) cc_final: 0.7423 (mtt) REVERT: B 74 GLU cc_start: 0.9693 (tm-30) cc_final: 0.9403 (tm-30) REVERT: C 50 TYR cc_start: 0.9112 (t80) cc_final: 0.8669 (t80) REVERT: D 105 GLU cc_start: 0.9204 (pp20) cc_final: 0.8690 (pp20) REVERT: D 109 HIS cc_start: 0.9128 (m170) cc_final: 0.8875 (m90) REVERT: E 50 GLU cc_start: 0.9541 (mp0) cc_final: 0.9335 (pm20) REVERT: E 51 ILE cc_start: 0.9685 (mt) cc_final: 0.9483 (mt) REVERT: E 59 GLU cc_start: 0.9041 (mp0) cc_final: 0.8602 (pm20) REVERT: E 67 PHE cc_start: 0.9433 (t80) cc_final: 0.9222 (t80) REVERT: E 82 LEU cc_start: 0.8329 (mm) cc_final: 0.8079 (mm) REVERT: E 90 MET cc_start: 0.9410 (mmp) cc_final: 0.8842 (mmp) REVERT: E 93 GLN cc_start: 0.9250 (tm-30) cc_final: 0.9042 (pt0) REVERT: E 104 PHE cc_start: 0.9282 (m-80) cc_final: 0.8972 (m-80) REVERT: E 120 MET cc_start: 0.8436 (mtm) cc_final: 0.7754 (mtt) REVERT: F 60 VAL cc_start: 0.9643 (t) cc_final: 0.9151 (t) REVERT: F 63 GLU cc_start: 0.9694 (mt-10) cc_final: 0.9434 (mt-10) REVERT: F 74 GLU cc_start: 0.9244 (pp20) cc_final: 0.8982 (pp20) REVERT: F 79 LYS cc_start: 0.9482 (tptp) cc_final: 0.9154 (tttt) REVERT: G 90 ASP cc_start: 0.8712 (t0) cc_final: 0.8299 (t0) REVERT: G 102 ILE cc_start: 0.8415 (mm) cc_final: 0.8129 (mm) REVERT: H 59 MET cc_start: 0.7643 (tpt) cc_final: 0.7248 (tmm) REVERT: H 108 LYS cc_start: 0.9291 (ptpp) cc_final: 0.8988 (ptpp) outliers start: 2 outliers final: 0 residues processed: 152 average time/residue: 0.1054 time to fit residues: 23.7122 Evaluate side-chains 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 40.0000 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 40.0000 chunk 41 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.028634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.021214 restraints weight = 174641.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.022054 restraints weight = 82059.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.022609 restraints weight = 48600.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.023001 restraints weight = 33088.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.023289 restraints weight = 24638.629| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14262 Z= 0.154 Angle : 0.660 8.766 20774 Z= 0.384 Chirality : 0.044 0.283 2360 Planarity : 0.004 0.067 1408 Dihedral : 32.982 179.592 4680 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.30), residues: 752 helix: 1.52 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.012 0.001 TYR D 121 PHE 0.035 0.002 PHE E 104 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (14262) covalent geometry : angle 0.66011 / 0.38 (20774) hydrogen bonds : bond 0.04872 / 3.29 ( 855) hydrogen bonds : angle 3.48005 / 2.48 ( 2102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9365 (mpp) cc_final: 0.9152 (mpp) REVERT: A 97 GLU cc_start: 0.9452 (pm20) cc_final: 0.9196 (pm20) REVERT: A 104 PHE cc_start: 0.9493 (m-80) cc_final: 0.9078 (m-80) REVERT: A 120 MET cc_start: 0.8071 (mtt) cc_final: 0.7405 (mtt) REVERT: B 74 GLU cc_start: 0.9712 (tm-30) cc_final: 0.9410 (tm-30) REVERT: B 91 LYS cc_start: 0.9295 (tmmt) cc_final: 0.8926 (pttm) REVERT: D 105 GLU cc_start: 0.9217 (pp20) cc_final: 0.8740 (pp20) REVERT: D 121 TYR cc_start: 0.9464 (t80) cc_final: 0.9147 (t80) REVERT: E 59 GLU cc_start: 0.9010 (mp0) cc_final: 0.8625 (pm20) REVERT: E 67 PHE cc_start: 0.9434 (t80) cc_final: 0.9223 (t80) REVERT: E 90 MET cc_start: 0.9455 (mmp) cc_final: 0.8833 (mmp) REVERT: E 120 MET cc_start: 0.8417 (mtm) cc_final: 0.7745 (mtt) REVERT: F 60 VAL cc_start: 0.9635 (t) cc_final: 0.9144 (t) REVERT: F 63 GLU cc_start: 0.9683 (mt-10) cc_final: 0.9435 (mt-10) REVERT: F 74 GLU cc_start: 0.9266 (pp20) cc_final: 0.8995 (pp20) REVERT: F 79 LYS cc_start: 0.9544 (tptp) cc_final: 0.9206 (tttt) REVERT: G 36 LYS cc_start: 0.9527 (mmmt) cc_final: 0.8999 (mmtm) REVERT: G 90 ASP cc_start: 0.8600 (t0) cc_final: 0.8197 (t0) REVERT: G 102 ILE cc_start: 0.8412 (mm) cc_final: 0.8117 (mm) REVERT: H 45 LEU cc_start: 0.9357 (tp) cc_final: 0.9151 (tp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1072 time to fit residues: 22.7881 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 chunk 33 optimal weight: 0.6980 chunk 77 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 0.0010 chunk 26 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.031936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.025087 restraints weight = 186673.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.025889 restraints weight = 86661.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.026460 restraints weight = 51363.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.026832 restraints weight = 34099.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.027055 restraints weight = 24918.365| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 14262 Z= 0.143 Angle : 0.666 8.072 20774 Z= 0.388 Chirality : 0.044 0.289 2360 Planarity : 0.004 0.065 1408 Dihedral : 32.887 179.547 4680 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 1.41 (0.29), residues: 752 helix: 1.49 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.36 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 20 TYR 0.012 0.002 TYR C 57 PHE 0.020 0.002 PHE G 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (14262) covalent geometry : angle 0.66565 / 0.39 (20774) hydrogen bonds : bond 0.04254 / 2.88 ( 855) hydrogen bonds : angle 3.49023 / 2.48 ( 2102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9413 (pm20) cc_final: 0.9082 (pm20) REVERT: A 104 PHE cc_start: 0.9466 (m-80) cc_final: 0.9016 (m-80) REVERT: A 120 MET cc_start: 0.8082 (mtt) cc_final: 0.7424 (mtt) REVERT: B 91 LYS cc_start: 0.9274 (tmmt) cc_final: 0.8895 (pttm) REVERT: D 105 GLU cc_start: 0.9105 (pp20) cc_final: 0.8740 (pp20) REVERT: D 109 HIS cc_start: 0.8790 (m90) cc_final: 0.7895 (m90) REVERT: D 121 TYR cc_start: 0.9415 (t80) cc_final: 0.9106 (t80) REVERT: E 59 GLU cc_start: 0.9014 (mp0) cc_final: 0.8516 (pm20) REVERT: E 67 PHE cc_start: 0.9411 (t80) cc_final: 0.9126 (t80) REVERT: E 82 LEU cc_start: 0.8246 (mm) cc_final: 0.7966 (mm) REVERT: E 93 GLN cc_start: 0.9374 (pm20) cc_final: 0.8954 (pm20) REVERT: E 120 MET cc_start: 0.8367 (mtm) cc_final: 0.7639 (mtt) REVERT: E 123 ASP cc_start: 0.9171 (m-30) cc_final: 0.8635 (m-30) REVERT: F 60 VAL cc_start: 0.9623 (t) cc_final: 0.9116 (t) REVERT: F 63 GLU cc_start: 0.9676 (mt-10) cc_final: 0.9439 (mt-10) REVERT: F 74 GLU cc_start: 0.9206 (pp20) cc_final: 0.8934 (pp20) REVERT: F 79 LYS cc_start: 0.9502 (tptp) cc_final: 0.9249 (tttt) REVERT: G 36 LYS cc_start: 0.9557 (mmmt) cc_final: 0.9033 (mmtm) REVERT: G 61 GLU cc_start: 0.9128 (pp20) cc_final: 0.8889 (pp20) REVERT: G 64 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9103 (tm-30) REVERT: G 90 ASP cc_start: 0.8639 (t0) cc_final: 0.8253 (t0) REVERT: G 102 ILE cc_start: 0.8403 (mm) cc_final: 0.8122 (mm) REVERT: H 108 LYS cc_start: 0.9288 (ptpp) cc_final: 0.8937 (ptpp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1053 time to fit residues: 22.7587 Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.031254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.024526 restraints weight = 192956.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.025348 restraints weight = 89257.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.025876 restraints weight = 51749.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.026251 restraints weight = 34755.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.026524 restraints weight = 25338.399| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14262 Z= 0.174 Angle : 0.674 8.718 20774 Z= 0.392 Chirality : 0.044 0.277 2360 Planarity : 0.005 0.067 1408 Dihedral : 32.862 179.671 4680 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 1.37 (0.30), residues: 752 helix: 1.44 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 42 TYR 0.010 0.001 TYR C 57 PHE 0.014 0.002 PHE G 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (14262) covalent geometry : angle 0.67443 / 0.39 (20774) hydrogen bonds : bond 0.05380 / 3.64 ( 855) hydrogen bonds : angle 3.59835 / 2.56 ( 2102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9319 (tp) cc_final: 0.9098 (tp) REVERT: A 90 MET cc_start: 0.9597 (mmm) cc_final: 0.9240 (mmm) REVERT: A 97 GLU cc_start: 0.9389 (pm20) cc_final: 0.9029 (pm20) REVERT: A 104 PHE cc_start: 0.9478 (m-80) cc_final: 0.9064 (m-80) REVERT: A 105 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9070 (tm-30) REVERT: A 106 ASP cc_start: 0.9455 (m-30) cc_final: 0.8859 (m-30) REVERT: A 120 MET cc_start: 0.8040 (mtt) cc_final: 0.7314 (mtt) REVERT: B 74 GLU cc_start: 0.9686 (tm-30) cc_final: 0.9406 (tm-30) REVERT: B 85 ASP cc_start: 0.8759 (m-30) cc_final: 0.8556 (m-30) REVERT: B 91 LYS cc_start: 0.9351 (tmmt) cc_final: 0.8924 (pttp) REVERT: D 105 GLU cc_start: 0.9115 (pp20) cc_final: 0.8755 (pp20) REVERT: D 109 HIS cc_start: 0.8848 (m90) cc_final: 0.8031 (m90) REVERT: D 121 TYR cc_start: 0.9444 (t80) cc_final: 0.9144 (t80) REVERT: E 51 ILE cc_start: 0.9662 (mt) cc_final: 0.9453 (mt) REVERT: E 59 GLU cc_start: 0.9007 (mp0) cc_final: 0.8549 (pm20) REVERT: E 104 PHE cc_start: 0.9355 (m-80) cc_final: 0.9152 (m-80) REVERT: E 105 GLU cc_start: 0.9149 (pp20) cc_final: 0.8891 (pp20) REVERT: E 106 ASP cc_start: 0.8663 (m-30) cc_final: 0.8120 (m-30) REVERT: E 120 MET cc_start: 0.8477 (mtm) cc_final: 0.7854 (mtt) REVERT: F 60 VAL cc_start: 0.9632 (t) cc_final: 0.9088 (t) REVERT: F 62 LEU cc_start: 0.9805 (mt) cc_final: 0.9438 (pp) REVERT: F 63 GLU cc_start: 0.9672 (mt-10) cc_final: 0.9298 (mt-10) REVERT: F 74 GLU cc_start: 0.9267 (pp20) cc_final: 0.9013 (pp20) REVERT: F 79 LYS cc_start: 0.9445 (tppt) cc_final: 0.9116 (tttt) REVERT: G 36 LYS cc_start: 0.9561 (mmmt) cc_final: 0.9056 (mmtm) REVERT: G 90 ASP cc_start: 0.8658 (t0) cc_final: 0.8275 (t0) REVERT: G 102 ILE cc_start: 0.8447 (mm) cc_final: 0.8169 (mm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1036 time to fit residues: 21.1297 Evaluate side-chains 100 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.031179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.024467 restraints weight = 192011.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.025280 restraints weight = 88137.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.025805 restraints weight = 51103.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.026169 restraints weight = 34090.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.026384 restraints weight = 25000.622| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14262 Z= 0.169 Angle : 0.685 8.643 20774 Z= 0.398 Chirality : 0.044 0.281 2360 Planarity : 0.005 0.066 1408 Dihedral : 32.877 179.406 4680 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.30), residues: 752 helix: 1.34 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.013 0.002 TYR A 99 PHE 0.024 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.17 (14262) covalent geometry : angle 0.68525 / 0.40 (20774) hydrogen bonds : bond 0.05125 / 3.47 ( 855) hydrogen bonds : angle 3.67697 / 2.61 ( 2102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9314 (tp) cc_final: 0.9075 (tp) REVERT: A 90 MET cc_start: 0.9606 (mmm) cc_final: 0.9302 (mmm) REVERT: A 97 GLU cc_start: 0.9271 (pm20) cc_final: 0.9045 (pm20) REVERT: A 104 PHE cc_start: 0.9492 (m-80) cc_final: 0.9061 (m-80) REVERT: A 120 MET cc_start: 0.8038 (mtt) cc_final: 0.7322 (mtt) REVERT: B 74 GLU cc_start: 0.9690 (tm-30) cc_final: 0.9413 (tm-30) REVERT: B 85 ASP cc_start: 0.8830 (m-30) cc_final: 0.8619 (m-30) REVERT: B 91 LYS cc_start: 0.9357 (tmmt) cc_final: 0.8947 (pttp) REVERT: D 105 GLU cc_start: 0.9128 (pp20) cc_final: 0.8804 (pp20) REVERT: D 109 HIS cc_start: 0.8909 (m90) cc_final: 0.8175 (m90) REVERT: E 59 GLU cc_start: 0.9034 (mp0) cc_final: 0.8576 (pm20) REVERT: E 93 GLN cc_start: 0.9388 (pm20) cc_final: 0.9103 (pm20) REVERT: E 120 MET cc_start: 0.8532 (mtm) cc_final: 0.7890 (mtt) REVERT: F 60 VAL cc_start: 0.9634 (t) cc_final: 0.9145 (t) REVERT: F 63 GLU cc_start: 0.9669 (mt-10) cc_final: 0.9443 (mt-10) REVERT: F 74 GLU cc_start: 0.9271 (pp20) cc_final: 0.9012 (pp20) REVERT: F 79 LYS cc_start: 0.9425 (tppt) cc_final: 0.9128 (tttt) REVERT: G 90 ASP cc_start: 0.8640 (t0) cc_final: 0.8204 (t0) REVERT: G 102 ILE cc_start: 0.8480 (mm) cc_final: 0.8217 (mm) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1077 time to fit residues: 22.2607 Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 50.0000 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.027967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.020727 restraints weight = 175842.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.021496 restraints weight = 85199.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.022019 restraints weight = 51326.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.022376 restraints weight = 35382.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.022611 restraints weight = 26637.510| |-----------------------------------------------------------------------------| r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14262 Z= 0.174 Angle : 0.682 8.981 20774 Z= 0.395 Chirality : 0.044 0.280 2360 Planarity : 0.005 0.066 1408 Dihedral : 32.876 179.580 4680 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.30), residues: 752 helix: 1.30 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.36 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 42 TYR 0.012 0.002 TYR A 99 PHE 0.027 0.002 PHE E 104 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 (14262) covalent geometry : angle 0.68226 / 0.40 (20774) hydrogen bonds : bond 0.05405 / 3.64 ( 855) hydrogen bonds : angle 3.70150 / 2.63 ( 2102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1728.57 seconds wall clock time: 30 minutes 53.30 seconds (1853.30 seconds total)