Starting phenix.real_space_refine on Wed Mar 4 18:20:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pfe_13373/03_2026/7pfe_13373.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pfe_13373/03_2026/7pfe_13373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pfe_13373/03_2026/7pfe_13373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pfe_13373/03_2026/7pfe_13373.map" model { file = "/net/cci-nas-00/data/ceres_data/7pfe_13373/03_2026/7pfe_13373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pfe_13373/03_2026/7pfe_13373.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 354 5.49 5 S 10 5.16 5 C 7617 2.51 5 N 2601 2.21 5 O 3298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13880 Number of models: 1 Model: "" Number of chains: 11 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: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3645 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "I" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3612 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "u" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 2.68, per 1000 atoms: 0.19 Number of scatterers: 13880 At special positions: 0 Unit cell: (133.35, 132.3, 119.7, 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 354 15.00 O 3298 8.00 N 2601 7.00 C 7617 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: 1.13 Conformation dependent library (CDL) restraints added in 431.3 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 70.6% alpha, 3.1% beta 174 base pairs and 308 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.783A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 removed outlier: 3.716A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 3.542A pdb=" N GLN b 27 " --> pdb=" O ASP b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 74 removed outlier: 4.607A 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 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.205A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.560A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 37 through 49 removed outlier: 3.889A 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: 3.551A pdb=" N ILE d 94 " --> pdb=" O THR d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 123 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.531A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (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 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 4.193A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.547A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.249A 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 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 104 through 124 removed outlier: 4.177A pdb=" N LYS h 108 " --> pdb=" O GLY h 104 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 51 removed outlier: 4.340A pdb=" N LEU u 42 " --> pdb=" O PRO u 38 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER u 50 " --> pdb=" O ALA u 46 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS u 51 " --> pdb=" O VAL u 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 58 through 69 Processing helix chain 'u' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.743A 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: 6.347A 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 77 through 78 Processing sheet with id=AA5, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.565A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.504A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (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: 7.226A 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 Processing sheet with id=AB1, first strand: chain 'u' and resid 56 through 57 433 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 444 hydrogen bonds 888 hydrogen bond angles 0 basepair planarities 174 basepair parallelities 308 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3118 1.34 - 1.46: 5388 1.46 - 1.58: 5614 1.58 - 1.71: 706 1.71 - 1.83: 20 Bond restraints: 14846 Sorted by residual: bond pdb=" CG GLU c 61 " pdb=" CD GLU c 61 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.27e+00 bond pdb=" C3' DG I 350 " pdb=" O3' DG I 350 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" CD GLU e 105 " pdb=" OE1 GLU e 105 " ideal model delta sigma weight residual 1.249 1.212 0.037 1.90e-02 2.77e+03 3.80e+00 bond pdb=" C LEU d 101 " pdb=" N LEU d 102 " ideal model delta sigma weight residual 1.327 1.282 0.045 2.31e-02 1.87e+03 3.75e+00 bond pdb=" CG GLU e 97 " pdb=" CD GLU e 97 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.60e+00 ... (remaining 14841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 20477 1.93 - 3.85: 925 3.85 - 5.78: 108 5.78 - 7.71: 38 7.71 - 9.63: 15 Bond angle restraints: 21563 Sorted by residual: angle pdb=" N GLU e 94 " pdb=" CA GLU e 94 " pdb=" CB GLU e 94 " ideal model delta sigma weight residual 110.28 118.56 -8.28 1.55e+00 4.16e-01 2.85e+01 angle pdb=" N GLU c 61 " pdb=" CA GLU c 61 " pdb=" CB GLU c 61 " ideal model delta sigma weight residual 110.16 117.60 -7.44 1.48e+00 4.57e-01 2.53e+01 angle pdb=" N GLU e 105 " pdb=" CA GLU e 105 " pdb=" CB GLU e 105 " ideal model delta sigma weight residual 110.28 118.04 -7.76 1.55e+00 4.16e-01 2.51e+01 angle pdb=" N GLU b 63 " pdb=" CA GLU b 63 " pdb=" CB GLU b 63 " ideal model delta sigma weight residual 110.22 117.49 -7.27 1.54e+00 4.22e-01 2.23e+01 angle pdb=" N GLU a 50 " pdb=" CA GLU a 50 " pdb=" CB GLU a 50 " ideal model delta sigma weight residual 110.28 117.59 -7.31 1.55e+00 4.16e-01 2.22e+01 ... (remaining 21558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6170 35.97 - 71.93: 1826 71.93 - 107.90: 25 107.90 - 143.86: 4 143.86 - 179.83: 2 Dihedral angle restraints: 8027 sinusoidal: 5596 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLU b 74 " pdb=" C GLU b 74 " pdb=" N HIS b 75 " pdb=" CA HIS b 75 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ILE b 50 " pdb=" C ILE b 50 " pdb=" N TYR b 51 " pdb=" CA TYR b 51 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LEU a 60 " pdb=" C LEU a 60 " pdb=" N LEU a 61 " pdb=" CA LEU a 61 " ideal model delta harmonic sigma weight residual -180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 8024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2074 0.065 - 0.129: 334 0.129 - 0.194: 37 0.194 - 0.259: 10 0.259 - 0.323: 1 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CA PHE e 104 " pdb=" N PHE e 104 " pdb=" C PHE e 104 " pdb=" CB PHE e 104 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+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 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 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 1.37e+00 ... (remaining 2453 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE a 104 " 0.018 2.00e-02 2.50e+03 2.09e-02 7.62e+00 pdb=" CG PHE a 104 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE a 104 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE a 104 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE a 104 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE a 104 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE a 104 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE c 79 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO c 80 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO c 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO c 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 99 " 0.214 9.50e-02 1.11e+02 9.63e-02 6.87e+00 pdb=" NE ARG d 99 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG d 99 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG d 99 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG d 99 " 0.001 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3060 2.79 - 3.32: 12862 3.32 - 3.85: 30171 3.85 - 4.37: 33418 4.37 - 4.90: 45752 Nonbonded interactions: 125263 Sorted by model distance: nonbonded pdb=" O GLN e 93 " pdb=" OG SER e 96 " model vdw 2.264 3.040 nonbonded pdb=" OE2 GLU u 52 " pdb=" OG SER u 54 " model vdw 2.270 3.040 nonbonded pdb=" OG SER c 40 " pdb=" O ARG c 42 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR d 90 " pdb=" OE1 GLU d 93 " model vdw 2.306 3.040 nonbonded pdb=" NE2 HIS a 113 " pdb=" OD1 ASP e 123 " model vdw 2.312 3.120 ... (remaining 125258 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.090 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 0.064 14846 Z= 0.305 Angle : 0.936 9.632 21563 Z= 0.535 Chirality : 0.049 0.323 2456 Planarity : 0.008 0.096 1498 Dihedral : 29.754 179.829 6461 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.43 (0.26), residues: 825 helix: 0.09 (0.20), residues: 566 sheet: -2.08 (1.53), residues: 10 loop : -0.80 (0.32), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG d 99 TYR 0.035 0.003 TYR f 72 PHE 0.048 0.003 PHE a 104 HIS 0.008 0.003 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00671 (14846) covalent geometry : angle 0.93626 (21563) hydrogen bonds : bond 0.11466 ( 877) hydrogen bonds : angle 4.99610 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9307 (mp0) cc_final: 0.9024 (mp0) REVERT: a 81 ASP cc_start: 0.8781 (t0) cc_final: 0.8269 (p0) REVERT: a 94 GLU cc_start: 0.9252 (mp0) cc_final: 0.8561 (mp0) REVERT: c 25 PHE cc_start: 0.8697 (m-80) cc_final: 0.8220 (m-80) REVERT: c 72 ASP cc_start: 0.9478 (m-30) cc_final: 0.9250 (m-30) REVERT: d 85 LYS cc_start: 0.9666 (mppt) cc_final: 0.9451 (mmtm) REVERT: d 99 ARG cc_start: 0.9093 (ttm110) cc_final: 0.8705 (mtp85) REVERT: d 106 LEU cc_start: 0.9478 (mt) cc_final: 0.9174 (mt) REVERT: d 113 GLU cc_start: 0.9130 (mp0) cc_final: 0.8823 (mp0) REVERT: e 50 GLU cc_start: 0.9653 (mp0) cc_final: 0.9278 (mp0) REVERT: e 54 TYR cc_start: 0.9479 (m-80) cc_final: 0.9278 (m-80) REVERT: e 90 MET cc_start: 0.9263 (tpt) cc_final: 0.8975 (tpt) REVERT: e 106 ASP cc_start: 0.9480 (m-30) cc_final: 0.9139 (m-30) REVERT: e 120 MET cc_start: 0.7446 (mtt) cc_final: 0.7055 (mtt) REVERT: e 124 ILE cc_start: 0.9539 (mt) cc_final: 0.9047 (mp) REVERT: f 44 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8998 (ttmt) REVERT: f 85 ASP cc_start: 0.8626 (m-30) cc_final: 0.8339 (m-30) REVERT: g 36 LYS cc_start: 0.9016 (mppt) cc_final: 0.8759 (mmtm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1247 time to fit residues: 28.5962 Evaluate side-chains 105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 84 ASN e 39 HIS e 55 GLN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.030686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.022731 restraints weight = 154118.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.023570 restraints weight = 73489.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.024153 restraints weight = 45289.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.024540 restraints weight = 32061.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.024792 restraints weight = 25018.502| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14846 Z= 0.176 Angle : 0.618 5.886 21563 Z= 0.370 Chirality : 0.035 0.145 2456 Planarity : 0.005 0.062 1498 Dihedral : 32.449 178.126 4809 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.87 % Allowed : 3.90 % Favored : 95.24 % 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: 0.84 (0.27), residues: 825 helix: 1.11 (0.21), residues: 580 sheet: -2.57 (1.33), residues: 10 loop : -0.54 (0.35), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 99 TYR 0.012 0.002 TYR h 40 PHE 0.005 0.001 PHE a 104 HIS 0.004 0.001 HIS a 113 Details of bonding type rmsd covalent geometry : bond 0.00374 (14846) covalent geometry : angle 0.61839 (21563) hydrogen bonds : bond 0.04232 ( 877) hydrogen bonds : angle 3.47258 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.341 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 50 GLU cc_start: 0.9316 (mp0) cc_final: 0.8981 (mp0) REVERT: a 60 LEU cc_start: 0.8764 (mt) cc_final: 0.7814 (mt) REVERT: a 94 GLU cc_start: 0.9213 (mp0) cc_final: 0.8885 (mm-30) REVERT: a 105 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8719 (mm-30) REVERT: a 120 MET cc_start: 0.8819 (mpp) cc_final: 0.8317 (mpp) REVERT: b 72 TYR cc_start: 0.9246 (m-80) cc_final: 0.9031 (m-80) REVERT: b 74 GLU cc_start: 0.9124 (pm20) cc_final: 0.8680 (pm20) REVERT: c 34 LEU cc_start: 0.9610 (mt) cc_final: 0.8949 (pp) REVERT: c 90 ASP cc_start: 0.8631 (t0) cc_final: 0.8328 (t0) REVERT: c 95 LYS cc_start: 0.9459 (ttmm) cc_final: 0.8999 (mppt) REVERT: d 85 LYS cc_start: 0.9696 (mppt) cc_final: 0.9475 (mmtm) REVERT: e 104 PHE cc_start: 0.9617 (m-10) cc_final: 0.9041 (m-80) REVERT: e 106 ASP cc_start: 0.9476 (m-30) cc_final: 0.9235 (m-30) REVERT: e 125 GLN cc_start: 0.9459 (mp10) cc_final: 0.9185 (mp10) REVERT: f 44 LYS cc_start: 0.9364 (ttmt) cc_final: 0.9092 (ttmt) REVERT: f 72 TYR cc_start: 0.9637 (m-80) cc_final: 0.9429 (m-80) REVERT: f 85 ASP cc_start: 0.8665 (m-30) cc_final: 0.8309 (m-30) REVERT: g 36 LYS cc_start: 0.8825 (mppt) cc_final: 0.8592 (mmtm) REVERT: g 73 ASN cc_start: 0.9520 (t0) cc_final: 0.9264 (t0) REVERT: h 68 ASP cc_start: 0.9300 (t0) cc_final: 0.9059 (t0) REVERT: h 105 GLU cc_start: 0.9285 (tp30) cc_final: 0.8831 (tp30) outliers start: 6 outliers final: 3 residues processed: 154 average time/residue: 0.1096 time to fit residues: 25.0673 Evaluate side-chains 108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 111 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 55 GLN ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.029345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.021659 restraints weight = 160390.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.022489 restraints weight = 76897.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.023056 restraints weight = 47040.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.023425 restraints weight = 32937.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.023694 restraints weight = 25641.822| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14846 Z= 0.233 Angle : 0.629 6.918 21563 Z= 0.373 Chirality : 0.035 0.145 2456 Planarity : 0.005 0.063 1498 Dihedral : 32.433 173.937 4809 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.43 % Allowed : 4.47 % Favored : 95.09 % 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: 1.10 (0.28), residues: 825 helix: 1.29 (0.21), residues: 584 sheet: -2.40 (1.30), residues: 10 loop : -0.45 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG g 29 TYR 0.014 0.002 TYR h 40 PHE 0.009 0.001 PHE f 100 HIS 0.005 0.001 HIS a 39 Details of bonding type rmsd covalent geometry : bond 0.00503 (14846) covalent geometry : angle 0.62888 (21563) hydrogen bonds : bond 0.05810 ( 877) hydrogen bonds : angle 3.52776 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 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: symmetry clash REVERT: a 50 GLU cc_start: 0.9313 (mp0) cc_final: 0.8974 (mp0) REVERT: a 60 LEU cc_start: 0.8761 (mt) cc_final: 0.8251 (mt) REVERT: a 97 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8701 (pm20) REVERT: c 90 ASP cc_start: 0.8683 (t0) cc_final: 0.8127 (t0) REVERT: c 95 LYS cc_start: 0.9473 (ttmm) cc_final: 0.9024 (mppt) REVERT: d 85 LYS cc_start: 0.9699 (mppt) cc_final: 0.9429 (mmtm) REVERT: d 99 ARG cc_start: 0.9314 (mtp85) cc_final: 0.8942 (ttm110) REVERT: d 113 GLU cc_start: 0.9202 (mp0) cc_final: 0.8909 (mp0) REVERT: e 90 MET cc_start: 0.9246 (mmp) cc_final: 0.8763 (mmt) REVERT: e 104 PHE cc_start: 0.9551 (m-10) cc_final: 0.9049 (m-80) REVERT: e 106 ASP cc_start: 0.9404 (m-30) cc_final: 0.9157 (m-30) REVERT: f 44 LYS cc_start: 0.9358 (ttmt) cc_final: 0.9147 (ttmt) REVERT: f 84 MET cc_start: 0.9007 (mmm) cc_final: 0.8755 (mmm) REVERT: f 85 ASP cc_start: 0.8713 (m-30) cc_final: 0.8431 (m-30) REVERT: g 61 GLU cc_start: 0.9516 (tm-30) cc_final: 0.9104 (tm-30) REVERT: h 52 THR cc_start: 0.8231 (m) cc_final: 0.7952 (p) REVERT: h 68 ASP cc_start: 0.9333 (t0) cc_final: 0.9106 (t0) REVERT: h 71 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8711 (mm-30) REVERT: h 105 GLU cc_start: 0.9176 (tp30) cc_final: 0.8959 (tp30) outliers start: 3 outliers final: 2 residues processed: 142 average time/residue: 0.1126 time to fit residues: 23.1986 Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.029082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.021517 restraints weight = 164673.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.022344 restraints weight = 79357.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.022897 restraints weight = 48536.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.023271 restraints weight = 34038.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.023531 restraints weight = 26445.535| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14846 Z= 0.231 Angle : 0.629 8.489 21563 Z= 0.373 Chirality : 0.035 0.147 2456 Planarity : 0.005 0.062 1498 Dihedral : 32.438 175.163 4809 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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 (0.28), residues: 825 helix: 1.44 (0.21), residues: 584 sheet: -2.15 (1.41), residues: 10 loop : -0.44 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 29 TYR 0.016 0.002 TYR h 40 PHE 0.008 0.001 PHE a 104 HIS 0.005 0.001 HIS a 39 Details of bonding type rmsd covalent geometry : bond 0.00498 (14846) covalent geometry : angle 0.62933 (21563) hydrogen bonds : bond 0.05463 ( 877) hydrogen bonds : angle 3.56800 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.362 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 50 GLU cc_start: 0.9304 (mp0) cc_final: 0.9001 (mp0) REVERT: a 60 LEU cc_start: 0.8754 (mt) cc_final: 0.7927 (mt) REVERT: a 123 ASP cc_start: 0.9271 (t0) cc_final: 0.9055 (t70) REVERT: b 74 GLU cc_start: 0.9258 (pm20) cc_final: 0.8792 (pm20) REVERT: c 25 PHE cc_start: 0.8473 (m-80) cc_final: 0.8195 (m-80) REVERT: c 90 ASP cc_start: 0.8542 (t0) cc_final: 0.8014 (t0) REVERT: c 95 LYS cc_start: 0.9462 (ttmm) cc_final: 0.9004 (mppt) REVERT: d 85 LYS cc_start: 0.9704 (mppt) cc_final: 0.9436 (mmtm) REVERT: d 99 ARG cc_start: 0.9298 (mtp85) cc_final: 0.8970 (ttm110) REVERT: e 54 TYR cc_start: 0.9441 (m-80) cc_final: 0.9220 (m-80) REVERT: e 90 MET cc_start: 0.9158 (mmp) cc_final: 0.8850 (mmm) REVERT: e 104 PHE cc_start: 0.9388 (m-10) cc_final: 0.8901 (m-80) REVERT: e 105 GLU cc_start: 0.9423 (pm20) cc_final: 0.9197 (pm20) REVERT: e 106 ASP cc_start: 0.9391 (m-30) cc_final: 0.9093 (m-30) REVERT: f 74 GLU cc_start: 0.9264 (pm20) cc_final: 0.9005 (pm20) REVERT: f 85 ASP cc_start: 0.8656 (m-30) cc_final: 0.8340 (m-30) REVERT: g 36 LYS cc_start: 0.8948 (mptt) cc_final: 0.8626 (mmtm) REVERT: g 61 GLU cc_start: 0.9499 (tm-30) cc_final: 0.9064 (tm-30) REVERT: h 52 THR cc_start: 0.8212 (m) cc_final: 0.7841 (p) REVERT: h 68 ASP cc_start: 0.9308 (t0) cc_final: 0.9100 (t0) REVERT: h 71 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8762 (mm-30) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1130 time to fit residues: 24.0165 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.0980 chunk 93 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS h 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.030051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.022317 restraints weight = 158824.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.023149 restraints weight = 76561.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.023701 restraints weight = 46880.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.024088 restraints weight = 33140.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.024340 restraints weight = 25782.783| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14846 Z= 0.165 Angle : 0.595 6.790 21563 Z= 0.354 Chirality : 0.034 0.150 2456 Planarity : 0.004 0.060 1498 Dihedral : 32.103 178.073 4809 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.72 % Allowed : 2.02 % Favored : 97.26 % 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: 1.58 (0.28), residues: 825 helix: 1.70 (0.21), residues: 580 sheet: -2.08 (1.47), residues: 10 loop : -0.39 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG h 92 TYR 0.014 0.001 TYR h 40 PHE 0.015 0.001 PHE d 65 HIS 0.006 0.001 HIS h 109 Details of bonding type rmsd covalent geometry : bond 0.00354 (14846) covalent geometry : angle 0.59482 (21563) hydrogen bonds : bond 0.03789 ( 877) hydrogen bonds : angle 3.31248 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.279 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 60 LEU cc_start: 0.8819 (mt) cc_final: 0.8113 (mt) REVERT: b 74 GLU cc_start: 0.9228 (pm20) cc_final: 0.8798 (pm20) REVERT: c 25 PHE cc_start: 0.8575 (m-80) cc_final: 0.8267 (m-80) REVERT: c 90 ASP cc_start: 0.8441 (t0) cc_final: 0.7902 (t0) REVERT: c 95 LYS cc_start: 0.9448 (ttmm) cc_final: 0.8931 (mppt) REVERT: d 35 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6251 (mt-10) REVERT: d 85 LYS cc_start: 0.9705 (mppt) cc_final: 0.9454 (mmtm) REVERT: d 99 ARG cc_start: 0.9250 (mtp85) cc_final: 0.8946 (ttm110) REVERT: d 113 GLU cc_start: 0.9208 (mp0) cc_final: 0.8842 (mp0) REVERT: e 50 GLU cc_start: 0.9652 (mp0) cc_final: 0.9306 (mp0) REVERT: e 90 MET cc_start: 0.9146 (mmp) cc_final: 0.8819 (mmm) REVERT: e 104 PHE cc_start: 0.9474 (m-10) cc_final: 0.8902 (m-80) REVERT: e 106 ASP cc_start: 0.9438 (m-30) cc_final: 0.9231 (m-30) REVERT: f 44 LYS cc_start: 0.9271 (ttmt) cc_final: 0.8970 (ttmt) REVERT: f 53 GLU cc_start: 0.9208 (tt0) cc_final: 0.8998 (pt0) REVERT: f 85 ASP cc_start: 0.8623 (m-30) cc_final: 0.8342 (m-30) REVERT: g 36 LYS cc_start: 0.8940 (mptt) cc_final: 0.8590 (mmtm) REVERT: g 61 GLU cc_start: 0.9521 (tm-30) cc_final: 0.9102 (tm-30) REVERT: h 47 GLN cc_start: 0.9280 (mt0) cc_final: 0.9059 (mt0) REVERT: h 71 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8828 (mm-30) outliers start: 5 outliers final: 2 residues processed: 151 average time/residue: 0.1133 time to fit residues: 24.8334 Evaluate side-chains 104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN e 108 ASN e 125 GLN h 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.021020 restraints weight = 166245.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.021800 restraints weight = 79840.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.022320 restraints weight = 49129.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.022714 restraints weight = 34882.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.022933 restraints weight = 26957.321| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14846 Z= 0.266 Angle : 0.639 8.178 21563 Z= 0.380 Chirality : 0.035 0.157 2456 Planarity : 0.005 0.057 1498 Dihedral : 32.284 175.275 4809 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.29 % Allowed : 2.31 % Favored : 97.40 % 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: 1.35 (0.28), residues: 825 helix: 1.52 (0.21), residues: 580 sheet: -1.97 (1.58), residues: 10 loop : -0.44 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 92 TYR 0.046 0.002 TYR f 98 PHE 0.011 0.001 PHE f 100 HIS 0.007 0.002 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.00574 (14846) covalent geometry : angle 0.63887 (21563) hydrogen bonds : bond 0.06402 ( 877) hydrogen bonds : angle 3.66394 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 60 LEU cc_start: 0.8744 (mt) cc_final: 0.7970 (mt) REVERT: a 81 ASP cc_start: 0.9064 (t0) cc_final: 0.8239 (p0) REVERT: a 105 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9189 (mm-30) REVERT: c 25 PHE cc_start: 0.8582 (m-80) cc_final: 0.8253 (m-80) REVERT: c 90 ASP cc_start: 0.8487 (t0) cc_final: 0.7901 (t0) REVERT: c 95 LYS cc_start: 0.9423 (ttmm) cc_final: 0.8923 (mppt) REVERT: d 35 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6310 (mt-10) REVERT: d 85 LYS cc_start: 0.9683 (mppt) cc_final: 0.9419 (mmtm) REVERT: d 99 ARG cc_start: 0.9283 (mtp85) cc_final: 0.8934 (ttm110) REVERT: e 50 GLU cc_start: 0.9603 (mp0) cc_final: 0.9305 (mp0) REVERT: e 90 MET cc_start: 0.9142 (mmp) cc_final: 0.8857 (mmm) REVERT: e 104 PHE cc_start: 0.9557 (m-10) cc_final: 0.9036 (m-80) REVERT: e 106 ASP cc_start: 0.9442 (m-30) cc_final: 0.8803 (m-30) REVERT: f 44 LYS cc_start: 0.9278 (ttmt) cc_final: 0.8933 (ttmt) REVERT: f 58 LEU cc_start: 0.9834 (tt) cc_final: 0.9462 (pp) REVERT: f 74 GLU cc_start: 0.9331 (pm20) cc_final: 0.9017 (pm20) REVERT: f 85 ASP cc_start: 0.8648 (m-30) cc_final: 0.8346 (m-30) REVERT: f 98 TYR cc_start: 0.8292 (m-80) cc_final: 0.7751 (m-10) REVERT: g 36 LYS cc_start: 0.8983 (mptt) cc_final: 0.8626 (mmtm) REVERT: g 61 GLU cc_start: 0.9476 (tm-30) cc_final: 0.9025 (tm-30) REVERT: h 52 THR cc_start: 0.8272 (m) cc_final: 0.7933 (p) REVERT: h 71 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8816 (mm-30) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 0.1178 time to fit residues: 22.7584 Evaluate side-chains 95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 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 = 0.028164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.020864 restraints weight = 164724.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.021675 restraints weight = 79891.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.022213 restraints weight = 48890.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.022572 restraints weight = 34382.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.022726 restraints weight = 26694.270| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14846 Z= 0.264 Angle : 0.650 9.406 21563 Z= 0.385 Chirality : 0.036 0.154 2456 Planarity : 0.005 0.062 1498 Dihedral : 32.402 177.359 4809 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.14 % Allowed : 1.01 % Favored : 98.85 % 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: 1.08 (0.28), residues: 825 helix: 1.29 (0.21), residues: 578 sheet: -1.92 (1.63), residues: 10 loop : -0.47 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 92 TYR 0.032 0.002 TYR f 98 PHE 0.016 0.001 PHE f 100 HIS 0.006 0.002 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.00573 (14846) covalent geometry : angle 0.64983 (21563) hydrogen bonds : bond 0.06215 ( 877) hydrogen bonds : angle 3.77666 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9296 (mp0) cc_final: 0.9062 (mp0) REVERT: a 81 ASP cc_start: 0.9108 (t0) cc_final: 0.8264 (p0) REVERT: a 105 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9188 (mm-30) REVERT: b 74 GLU cc_start: 0.9232 (pm20) cc_final: 0.8819 (pm20) REVERT: c 25 PHE cc_start: 0.8632 (m-80) cc_final: 0.8252 (m-80) REVERT: c 90 ASP cc_start: 0.8489 (t0) cc_final: 0.7925 (t0) REVERT: c 95 LYS cc_start: 0.9454 (ttmm) cc_final: 0.9000 (mppt) REVERT: d 85 LYS cc_start: 0.9683 (mppt) cc_final: 0.9417 (mmtm) REVERT: d 99 ARG cc_start: 0.9269 (mtp85) cc_final: 0.8880 (ttm110) REVERT: d 113 GLU cc_start: 0.9270 (mp0) cc_final: 0.8893 (mp0) REVERT: e 50 GLU cc_start: 0.9677 (mp0) cc_final: 0.9378 (mp0) REVERT: e 104 PHE cc_start: 0.9524 (m-10) cc_final: 0.8964 (m-80) REVERT: e 105 GLU cc_start: 0.9476 (pm20) cc_final: 0.9196 (pm20) REVERT: e 106 ASP cc_start: 0.9102 (m-30) cc_final: 0.8811 (m-30) REVERT: f 44 LYS cc_start: 0.9272 (ttmt) cc_final: 0.8985 (ttmt) REVERT: f 58 LEU cc_start: 0.9836 (tt) cc_final: 0.9569 (pp) REVERT: f 85 ASP cc_start: 0.8654 (m-30) cc_final: 0.8313 (m-30) REVERT: f 98 TYR cc_start: 0.8235 (m-80) cc_final: 0.7875 (m-10) REVERT: g 36 LYS cc_start: 0.8981 (mptt) cc_final: 0.8625 (mmtm) REVERT: g 61 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9017 (tm-30) REVERT: h 52 THR cc_start: 0.8237 (m) cc_final: 0.7879 (p) REVERT: h 71 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8802 (mm-30) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1198 time to fit residues: 22.5314 Evaluate side-chains 97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN e 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.028956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.021482 restraints weight = 161851.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.022292 restraints weight = 78513.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.022848 restraints weight = 48443.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.023210 restraints weight = 34185.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.023457 restraints weight = 26700.651| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14846 Z= 0.194 Angle : 0.616 8.235 21563 Z= 0.367 Chirality : 0.035 0.165 2456 Planarity : 0.004 0.056 1498 Dihedral : 32.274 176.919 4809 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.14 % Allowed : 1.44 % Favored : 98.41 % 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: 1.25 (0.28), residues: 825 helix: 1.45 (0.21), residues: 580 sheet: -1.86 (1.61), residues: 10 loop : -0.51 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 23 TYR 0.025 0.002 TYR f 98 PHE 0.011 0.001 PHE f 100 HIS 0.005 0.001 HIS a 113 Details of bonding type rmsd covalent geometry : bond 0.00420 (14846) covalent geometry : angle 0.61645 (21563) hydrogen bonds : bond 0.04595 ( 877) hydrogen bonds : angle 3.62739 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9312 (mp0) cc_final: 0.9039 (mp0) REVERT: a 60 LEU cc_start: 0.8676 (mt) cc_final: 0.8138 (mt) REVERT: a 97 GLU cc_start: 0.9309 (pm20) cc_final: 0.8984 (pm20) REVERT: a 105 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9228 (mm-30) REVERT: a 117 VAL cc_start: 0.9090 (m) cc_final: 0.8773 (p) REVERT: c 25 PHE cc_start: 0.8635 (m-80) cc_final: 0.8250 (m-80) REVERT: c 90 ASP cc_start: 0.8434 (t0) cc_final: 0.8099 (t0) REVERT: c 95 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9015 (mppt) REVERT: d 85 LYS cc_start: 0.9683 (mppt) cc_final: 0.9432 (mmtm) REVERT: d 99 ARG cc_start: 0.9281 (mtp85) cc_final: 0.8930 (ttm110) REVERT: d 113 GLU cc_start: 0.9201 (mp0) cc_final: 0.8786 (mp0) REVERT: e 50 GLU cc_start: 0.9666 (mp0) cc_final: 0.9252 (mp0) REVERT: e 104 PHE cc_start: 0.9471 (m-10) cc_final: 0.8919 (m-80) REVERT: e 106 ASP cc_start: 0.9066 (m-30) cc_final: 0.8553 (m-30) REVERT: f 58 LEU cc_start: 0.9821 (tt) cc_final: 0.9417 (pp) REVERT: f 59 LYS cc_start: 0.9819 (ptmm) cc_final: 0.9524 (ptmm) REVERT: f 85 ASP cc_start: 0.8629 (m-30) cc_final: 0.8306 (m-30) REVERT: f 98 TYR cc_start: 0.8146 (m-80) cc_final: 0.7819 (m-10) REVERT: g 61 GLU cc_start: 0.9500 (tm-30) cc_final: 0.9073 (tm-30) REVERT: h 68 ASP cc_start: 0.9311 (t0) cc_final: 0.9109 (t0) REVERT: h 71 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8836 (mm-30) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1108 time to fit residues: 22.8118 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.029142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.021662 restraints weight = 162274.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.022498 restraints weight = 77378.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.023066 restraints weight = 46975.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.023432 restraints weight = 32956.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.023684 restraints weight = 25666.330| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14846 Z= 0.187 Angle : 0.621 7.239 21563 Z= 0.370 Chirality : 0.035 0.201 2456 Planarity : 0.004 0.057 1498 Dihedral : 32.113 175.786 4809 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.28), residues: 825 helix: 1.48 (0.21), residues: 580 sheet: -1.81 (1.62), residues: 10 loop : -0.56 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 23 TYR 0.026 0.002 TYR e 54 PHE 0.007 0.001 PHE f 100 HIS 0.005 0.001 HIS a 113 Details of bonding type rmsd covalent geometry : bond 0.00403 (14846) covalent geometry : angle 0.62072 (21563) hydrogen bonds : bond 0.04364 ( 877) hydrogen bonds : angle 3.70828 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 50 GLU cc_start: 0.9302 (mp0) cc_final: 0.9062 (pm20) REVERT: a 60 LEU cc_start: 0.8693 (mt) cc_final: 0.8379 (mt) REVERT: a 81 ASP cc_start: 0.9091 (t0) cc_final: 0.8299 (p0) REVERT: a 97 GLU cc_start: 0.9277 (pm20) cc_final: 0.8994 (pm20) REVERT: a 104 PHE cc_start: 0.9613 (m-80) cc_final: 0.9366 (m-80) REVERT: a 105 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9237 (mm-30) REVERT: a 117 VAL cc_start: 0.9116 (m) cc_final: 0.8813 (p) REVERT: b 74 GLU cc_start: 0.9232 (pm20) cc_final: 0.9001 (pm20) REVERT: c 25 PHE cc_start: 0.8640 (m-80) cc_final: 0.8204 (m-80) REVERT: c 90 ASP cc_start: 0.8218 (t0) cc_final: 0.7837 (t0) REVERT: c 95 LYS cc_start: 0.9428 (ttmm) cc_final: 0.8938 (mppt) REVERT: d 85 LYS cc_start: 0.9676 (mppt) cc_final: 0.9429 (mmtm) REVERT: d 99 ARG cc_start: 0.9276 (mtp85) cc_final: 0.8889 (ttm110) REVERT: d 113 GLU cc_start: 0.9198 (mp0) cc_final: 0.8789 (mp0) REVERT: e 50 GLU cc_start: 0.9660 (mp0) cc_final: 0.9318 (mp0) REVERT: e 104 PHE cc_start: 0.9410 (m-10) cc_final: 0.8798 (m-80) REVERT: e 105 GLU cc_start: 0.9485 (pm20) cc_final: 0.9199 (pm20) REVERT: e 106 ASP cc_start: 0.9037 (m-30) cc_final: 0.8778 (m-30) REVERT: e 120 MET cc_start: 0.7077 (mtt) cc_final: 0.6489 (mtt) REVERT: e 124 ILE cc_start: 0.9519 (tt) cc_final: 0.9207 (tt) REVERT: f 44 LYS cc_start: 0.9250 (ttmt) cc_final: 0.8989 (ttmt) REVERT: f 58 LEU cc_start: 0.9818 (tt) cc_final: 0.9429 (pp) REVERT: f 59 LYS cc_start: 0.9812 (ptmm) cc_final: 0.9524 (ptmm) REVERT: f 85 ASP cc_start: 0.8654 (m-30) cc_final: 0.8356 (m-30) REVERT: f 98 TYR cc_start: 0.7793 (m-80) cc_final: 0.7506 (m-80) REVERT: g 61 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9099 (tm-30) REVERT: h 68 ASP cc_start: 0.9313 (t0) cc_final: 0.9073 (t0) REVERT: h 71 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8840 (mm-30) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1066 time to fit residues: 22.5262 Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.021137 restraints weight = 164594.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.021950 restraints weight = 78953.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.022510 restraints weight = 48331.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.022869 restraints weight = 33720.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.023117 restraints weight = 26125.330| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14846 Z= 0.234 Angle : 0.641 7.898 21563 Z= 0.380 Chirality : 0.035 0.170 2456 Planarity : 0.005 0.053 1498 Dihedral : 32.199 174.818 4809 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.14 % Allowed : 0.58 % Favored : 99.28 % 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: 1.22 (0.28), residues: 825 helix: 1.45 (0.21), residues: 580 sheet: -1.73 (1.70), residues: 10 loop : -0.62 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 23 TYR 0.021 0.002 TYR h 40 PHE 0.011 0.001 PHE d 65 HIS 0.007 0.001 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.00508 (14846) covalent geometry : angle 0.64053 (21563) hydrogen bonds : bond 0.05617 ( 877) hydrogen bonds : angle 3.77539 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 104 PHE cc_start: 0.9652 (m-80) cc_final: 0.9426 (m-80) REVERT: a 105 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9161 (mm-30) REVERT: a 117 VAL cc_start: 0.9156 (m) cc_final: 0.8851 (p) REVERT: b 74 GLU cc_start: 0.9260 (pm20) cc_final: 0.9030 (pm20) REVERT: c 25 PHE cc_start: 0.8663 (m-80) cc_final: 0.8240 (m-80) REVERT: c 90 ASP cc_start: 0.8434 (t0) cc_final: 0.8089 (t0) REVERT: c 95 LYS cc_start: 0.9417 (ttmm) cc_final: 0.8949 (mppt) REVERT: d 85 LYS cc_start: 0.9669 (mppt) cc_final: 0.9422 (mmtm) REVERT: d 99 ARG cc_start: 0.9262 (mtp85) cc_final: 0.8827 (ttm110) REVERT: d 113 GLU cc_start: 0.9181 (mp0) cc_final: 0.8819 (mp0) REVERT: e 50 GLU cc_start: 0.9658 (mp0) cc_final: 0.9270 (mp0) REVERT: e 104 PHE cc_start: 0.9445 (m-10) cc_final: 0.8852 (m-80) REVERT: e 105 GLU cc_start: 0.9493 (pm20) cc_final: 0.9210 (pm20) REVERT: e 106 ASP cc_start: 0.9080 (m-30) cc_final: 0.8803 (m-30) REVERT: f 44 LYS cc_start: 0.9226 (ttmt) cc_final: 0.8889 (ttmt) REVERT: f 58 LEU cc_start: 0.9834 (tt) cc_final: 0.9462 (pp) REVERT: f 59 LYS cc_start: 0.9816 (ptmm) cc_final: 0.9509 (ptmm) REVERT: f 85 ASP cc_start: 0.8636 (m-30) cc_final: 0.8295 (m-30) REVERT: f 98 TYR cc_start: 0.8077 (m-80) cc_final: 0.7716 (m-10) REVERT: g 61 GLU cc_start: 0.9510 (tm-30) cc_final: 0.9063 (tm-30) REVERT: h 52 THR cc_start: 0.8069 (m) cc_final: 0.7722 (p) REVERT: h 68 ASP cc_start: 0.9311 (t0) cc_final: 0.9079 (t0) REVERT: h 71 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8822 (mm-30) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1104 time to fit residues: 22.8387 Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 93 GLN a 108 ASN ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.029406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.022038 restraints weight = 160837.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.022895 restraints weight = 76089.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.023481 restraints weight = 45961.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.023866 restraints weight = 31918.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.024139 restraints weight = 24525.010| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14846 Z= 0.168 Angle : 0.617 8.790 21563 Z= 0.366 Chirality : 0.035 0.194 2456 Planarity : 0.004 0.055 1498 Dihedral : 32.032 175.780 4809 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.28), residues: 825 helix: 1.53 (0.21), residues: 580 sheet: -1.87 (1.67), residues: 10 loop : -0.63 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 23 TYR 0.027 0.002 TYR e 54 PHE 0.008 0.001 PHE d 65 HIS 0.006 0.001 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (14846) covalent geometry : angle 0.61744 (21563) hydrogen bonds : bond 0.03892 ( 877) hydrogen bonds : angle 3.60159 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1780.69 seconds wall clock time: 31 minutes 44.65 seconds (1904.65 seconds total)