Starting phenix.real_space_refine on Sat May 2 12:26:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxz_61882/05_2026/9jxz_61882.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxz_61882/05_2026/9jxz_61882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jxz_61882/05_2026/9jxz_61882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxz_61882/05_2026/9jxz_61882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jxz_61882/05_2026/9jxz_61882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxz_61882/05_2026/9jxz_61882.map" } resolution = 3.31 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= -0.004 sd= 0.133 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 37 5.16 5 C 3153 2.51 5 N 753 2.21 5 O 900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4846 Number of models: 1 Model: "" Number of chains: 10 Chain: "a" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "b" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "m" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 285 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "n" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 310 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "b" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'CLR': 2, 'LPE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 30 Chain: "d" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'LPE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 19 Time building chain proxies: 0.96, per 1000 atoms: 0.20 Number of scatterers: 4846 At special positions: 0 Unit cell: (74.76, 87.36, 106.68, 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 37 16.00 P 3 15.00 O 900 8.00 N 753 7.00 C 3153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.02 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 107.4 milliseconds 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1114 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 41.0% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'a' and resid 30 through 54 removed outlier: 4.373A pdb=" N ILE a 38 " --> pdb=" O LEU a 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY a 43 " --> pdb=" O LEU a 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 55 removed outlier: 3.583A pdb=" N ARG b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 126 Processing helix chain 'e' and resid 126 through 153 removed outlier: 3.708A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS e 153 " --> pdb=" O TYR e 149 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.645A pdb=" N ALA f 108 " --> pdb=" O PRO f 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 153 Processing helix chain 'g' and resid 76 through 80 Processing helix chain 'g' and resid 111 through 140 removed outlier: 3.986A pdb=" N ILE g 115 " --> pdb=" O ASN g 111 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER g 116 " --> pdb=" O ALA g 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 258 through 289 Processing helix chain 'n' and resid 252 through 288 removed outlier: 3.592A pdb=" N CYS n 283 " --> pdb=" O ILE n 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'd' and resid 85 through 86 removed outlier: 5.724A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 85 through 86 removed outlier: 5.724A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS e 64 " --> pdb=" O HIS e 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.547A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR e 44 " --> pdb=" O SER e 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 38 through 41 Processing sheet with id=AA7, first strand: chain 'f' and resid 64 through 65 removed outlier: 3.516A pdb=" N GLN f 60 " --> pdb=" O VAL f 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU f 112 " --> pdb=" O TYR f 96 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS g 87 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TYR g 85 " --> pdb=" O PRO g 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.735A pdb=" N TYR g 34 " --> pdb=" O LEU g 43 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU g 74 " --> pdb=" O VAL g 42 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1477 1.34 - 1.47: 1168 1.47 - 1.59: 2237 1.59 - 1.71: 6 1.71 - 1.83: 51 Bond restraints: 4939 Sorted by residual: bond pdb=" O33 LPE b 202 " pdb=" P LPE b 202 " ideal model delta sigma weight residual 1.673 1.605 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O33 LPE b 203 " pdb=" P LPE b 203 " ideal model delta sigma weight residual 1.673 1.606 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O33 LPE d 201 " pdb=" P LPE d 201 " ideal model delta sigma weight residual 1.673 1.607 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O3 LPE b 203 " pdb=" P LPE b 203 " ideal model delta sigma weight residual 1.662 1.606 0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" O3 LPE b 202 " pdb=" P LPE b 202 " ideal model delta sigma weight residual 1.662 1.606 0.056 2.00e-02 2.50e+03 7.94e+00 ... (remaining 4934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 6493 1.65 - 3.29: 154 3.29 - 4.94: 23 4.94 - 6.59: 19 6.59 - 8.23: 5 Bond angle restraints: 6694 Sorted by residual: angle pdb=" N ILE f 75 " pdb=" CA ILE f 75 " pdb=" C ILE f 75 " ideal model delta sigma weight residual 113.53 107.37 6.16 9.80e-01 1.04e+00 3.95e+01 angle pdb=" C ASP f 72 " pdb=" N LYS f 73 " pdb=" CA LYS f 73 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" N ILE e 140 " pdb=" CA ILE e 140 " pdb=" CB ILE e 140 " ideal model delta sigma weight residual 110.58 115.15 -4.57 1.50e+00 4.44e-01 9.27e+00 angle pdb=" CA ILE e 140 " pdb=" CB ILE e 140 " pdb=" CG1 ILE e 140 " ideal model delta sigma weight residual 110.40 115.55 -5.15 1.70e+00 3.46e-01 9.19e+00 angle pdb=" C GLU e 120 " pdb=" N ASN e 121 " pdb=" CA ASN e 121 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.37e+00 ... (remaining 6689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 2660 17.54 - 35.08: 310 35.08 - 52.63: 83 52.63 - 70.17: 14 70.17 - 87.71: 5 Dihedral angle restraints: 3072 sinusoidal: 1334 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS f 119 " pdb=" SG CYS f 119 " pdb=" SG CYS f 122 " pdb=" CB CYS f 122 " ideal model delta sinusoidal sigma weight residual -86.00 -159.96 73.96 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS g 46 " pdb=" SG CYS g 46 " pdb=" SG CYS g 87 " pdb=" CB CYS g 87 " ideal model delta sinusoidal sigma weight residual -86.00 -132.55 46.55 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA ASP f 72 " pdb=" C ASP f 72 " pdb=" N LYS f 73 " pdb=" CA LYS f 73 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 3069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 480 0.030 - 0.060: 202 0.060 - 0.090: 69 0.090 - 0.119: 25 0.119 - 0.149: 5 Chirality restraints: 781 Sorted by residual: chirality pdb=" CA ASN f 121 " pdb=" N ASN f 121 " pdb=" C ASN f 121 " pdb=" CB ASN f 121 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ASN e 121 " pdb=" N ASN e 121 " pdb=" C ASN e 121 " pdb=" CB ASN e 121 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE f 57 " pdb=" N ILE f 57 " pdb=" C ILE f 57 " pdb=" CB ILE f 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 778 not shown) Planarity restraints: 808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP g 58 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.03e+00 pdb=" C ASP g 58 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP g 58 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY g 59 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE d 24 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO d 25 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO d 25 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO d 25 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS e 104 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO e 105 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO e 105 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO e 105 " -0.020 5.00e-02 4.00e+02 ... (remaining 805 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 143 2.70 - 3.25: 4771 3.25 - 3.80: 7401 3.80 - 4.35: 8990 4.35 - 4.90: 15371 Nonbonded interactions: 36676 Sorted by model distance: nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THR d 42 " pdb=" O ARG d 72 " model vdw 2.174 3.040 nonbonded pdb=" ND2 ASN d 36 " pdb=" O THR d 56 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASN g 111 " pdb=" OG1 THR g 114 " model vdw 2.272 3.040 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.288 3.040 ... (remaining 36671 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' and resid 27 through 55) selection = (chain 'b' and resid 27 through 55) } ncs_group { reference = chain 'e' selection = (chain 'f' and resid 33 through 153) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.270 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.005 0.068 4947 Z= 0.222 Angle : 0.683 8.235 6710 Z= 0.350 Chirality : 0.039 0.149 781 Planarity : 0.004 0.043 808 Dihedral : 15.713 87.712 1934 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.39 % Allowed : 13.94 % Favored : 82.67 % 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: 0.14 (0.36), residues: 581 helix: 3.26 (0.32), residues: 226 sheet: -1.33 (0.53), residues: 97 loop : -2.43 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 117 TYR 0.010 0.001 TYR e 36 PHE 0.013 0.002 PHE b 55 TRP 0.010 0.001 TRP g 72 HIS 0.002 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 4939) covalent geometry : angle 0.68065 ( 6694) SS BOND : bond 0.00402 ( 8) SS BOND : angle 1.33935 ( 16) hydrogen bonds : bond 0.14510 ( 247) hydrogen bonds : angle 6.06090 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.160 Fit side-chains REVERT: g 140 ASP cc_start: 0.6767 (t0) cc_final: 0.6306 (t0) outliers start: 18 outliers final: 17 residues processed: 98 average time/residue: 0.0625 time to fit residues: 7.9182 Evaluate side-chains 103 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 69 ASP Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 106 ASN Chi-restraints excluded: chain n residue 281 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN f 81 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.216653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.182982 restraints weight = 5662.268| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.04 r_work: 0.3774 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4947 Z= 0.131 Angle : 0.539 6.101 6710 Z= 0.284 Chirality : 0.039 0.149 781 Planarity : 0.004 0.040 808 Dihedral : 8.807 55.627 852 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.01 % Allowed : 14.50 % Favored : 82.49 % 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: 0.40 (0.36), residues: 581 helix: 3.57 (0.31), residues: 226 sheet: -1.40 (0.53), residues: 98 loop : -2.28 (0.34), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 117 TYR 0.010 0.001 TYR e 36 PHE 0.010 0.001 PHE g 56 TRP 0.010 0.001 TRP f 59 HIS 0.002 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4939) covalent geometry : angle 0.53739 ( 6694) SS BOND : bond 0.00388 ( 8) SS BOND : angle 1.01441 ( 16) hydrogen bonds : bond 0.04791 ( 247) hydrogen bonds : angle 4.50174 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: g 140 ASP cc_start: 0.6565 (t0) cc_final: 0.6231 (t0) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.0675 time to fit residues: 8.8663 Evaluate side-chains 97 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain g residue 64 PHE Chi-restraints excluded: chain n residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.215345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.181255 restraints weight = 5615.682| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.06 r_work: 0.3753 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4947 Z= 0.143 Angle : 0.544 6.241 6710 Z= 0.285 Chirality : 0.039 0.149 781 Planarity : 0.004 0.063 808 Dihedral : 8.521 59.776 834 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.52 % Allowed : 15.25 % Favored : 80.23 % 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: 0.37 (0.36), residues: 581 helix: 3.55 (0.31), residues: 226 sheet: -1.56 (0.52), residues: 98 loop : -2.24 (0.34), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 52 TYR 0.010 0.001 TYR e 113 PHE 0.010 0.001 PHE g 118 TRP 0.010 0.001 TRP g 72 HIS 0.004 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4939) covalent geometry : angle 0.54291 ( 6694) SS BOND : bond 0.00365 ( 8) SS BOND : angle 0.77019 ( 16) hydrogen bonds : bond 0.04971 ( 247) hydrogen bonds : angle 4.25001 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.137 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 104 average time/residue: 0.0734 time to fit residues: 9.7092 Evaluate side-chains 106 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 128 MET Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 64 PHE Chi-restraints excluded: chain n residue 267 LEU Chi-restraints excluded: chain n residue 281 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.214678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.180424 restraints weight = 5658.528| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.00 r_work: 0.3748 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4947 Z= 0.134 Angle : 0.536 7.421 6710 Z= 0.280 Chirality : 0.039 0.147 781 Planarity : 0.003 0.038 808 Dihedral : 7.956 49.870 834 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.71 % Allowed : 15.82 % Favored : 79.47 % 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: 0.47 (0.36), residues: 581 helix: 3.65 (0.31), residues: 226 sheet: -1.49 (0.53), residues: 98 loop : -2.20 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 117 TYR 0.010 0.001 TYR e 113 PHE 0.010 0.001 PHE f 87 TRP 0.011 0.001 TRP f 59 HIS 0.004 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4939) covalent geometry : angle 0.53486 ( 6694) SS BOND : bond 0.00433 ( 8) SS BOND : angle 0.77135 ( 16) hydrogen bonds : bond 0.04722 ( 247) hydrogen bonds : angle 4.05694 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: e 91 GLU cc_start: 0.7575 (tp30) cc_final: 0.6866 (tt0) REVERT: f 128 MET cc_start: 0.7113 (mmt) cc_final: 0.6241 (ptt) outliers start: 25 outliers final: 21 residues processed: 106 average time/residue: 0.0736 time to fit residues: 9.9819 Evaluate side-chains 109 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain n residue 267 LEU Chi-restraints excluded: chain n residue 281 THR Chi-restraints excluded: chain n residue 288 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.215736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181802 restraints weight = 5666.035| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.99 r_work: 0.3775 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4947 Z= 0.143 Angle : 0.549 7.369 6710 Z= 0.286 Chirality : 0.039 0.148 781 Planarity : 0.004 0.061 808 Dihedral : 7.753 48.038 832 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.40 % Allowed : 15.07 % Favored : 78.53 % 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: 0.46 (0.36), residues: 581 helix: 3.55 (0.31), residues: 226 sheet: -0.95 (0.57), residues: 82 loop : -2.31 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 117 TYR 0.011 0.001 TYR e 113 PHE 0.011 0.001 PHE f 87 TRP 0.012 0.001 TRP f 59 HIS 0.004 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4939) covalent geometry : angle 0.54807 ( 6694) SS BOND : bond 0.00363 ( 8) SS BOND : angle 0.73813 ( 16) hydrogen bonds : bond 0.04929 ( 247) hydrogen bonds : angle 4.07631 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: e 91 GLU cc_start: 0.7425 (tp30) cc_final: 0.6840 (tt0) REVERT: e 115 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.7066 (ttm110) REVERT: f 128 MET cc_start: 0.7044 (mmt) cc_final: 0.6279 (ptt) REVERT: g 36 TYR cc_start: 0.4111 (OUTLIER) cc_final: 0.3509 (m-10) outliers start: 34 outliers final: 28 residues processed: 113 average time/residue: 0.0751 time to fit residues: 10.7566 Evaluate side-chains 116 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 128 MET Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 64 PHE Chi-restraints excluded: chain g residue 87 CYS Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain n residue 267 LEU Chi-restraints excluded: chain n residue 281 THR Chi-restraints excluded: chain n residue 288 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 31 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.211424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.168373 restraints weight = 5726.300| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.62 r_work: 0.3810 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4947 Z= 0.125 Angle : 0.528 6.992 6710 Z= 0.277 Chirality : 0.039 0.144 781 Planarity : 0.004 0.052 808 Dihedral : 7.500 52.649 832 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 6.59 % Allowed : 15.63 % Favored : 77.78 % 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: 0.61 (0.36), residues: 581 helix: 3.69 (0.31), residues: 226 sheet: -0.56 (0.63), residues: 71 loop : -2.30 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 117 TYR 0.009 0.001 TYR n 266 PHE 0.008 0.001 PHE f 87 TRP 0.013 0.001 TRP f 59 HIS 0.005 0.001 HIS f 81 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4939) covalent geometry : angle 0.52749 ( 6694) SS BOND : bond 0.00309 ( 8) SS BOND : angle 0.68648 ( 16) hydrogen bonds : bond 0.04547 ( 247) hydrogen bonds : angle 3.90209 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: e 91 GLU cc_start: 0.7466 (tp30) cc_final: 0.6874 (tt0) REVERT: f 128 MET cc_start: 0.7018 (mmt) cc_final: 0.6195 (ptt) REVERT: g 36 TYR cc_start: 0.4159 (OUTLIER) cc_final: 0.3546 (m-10) outliers start: 35 outliers final: 28 residues processed: 112 average time/residue: 0.0673 time to fit residues: 9.7422 Evaluate side-chains 115 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 64 PHE Chi-restraints excluded: chain g residue 87 CYS Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain n residue 267 LEU Chi-restraints excluded: chain n residue 281 THR Chi-restraints excluded: chain n residue 282 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 0.4980 chunk 33 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.218763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.185605 restraints weight = 5677.615| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.01 r_work: 0.3799 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4947 Z= 0.108 Angle : 0.504 5.613 6710 Z= 0.266 Chirality : 0.038 0.144 781 Planarity : 0.003 0.048 808 Dihedral : 7.225 56.438 832 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.27 % Allowed : 17.33 % Favored : 77.40 % 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: 0.77 (0.36), residues: 581 helix: 3.85 (0.31), residues: 226 sheet: -0.44 (0.64), residues: 71 loop : -2.25 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 117 TYR 0.008 0.001 TYR n 266 PHE 0.008 0.001 PHE f 87 TRP 0.012 0.001 TRP f 59 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4939) covalent geometry : angle 0.50303 ( 6694) SS BOND : bond 0.00299 ( 8) SS BOND : angle 0.74351 ( 16) hydrogen bonds : bond 0.04004 ( 247) hydrogen bonds : angle 3.72698 ( 714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: e 36 TYR cc_start: 0.5725 (m-80) cc_final: 0.5524 (m-80) REVERT: e 48 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.6937 (p) REVERT: e 91 GLU cc_start: 0.7377 (tp30) cc_final: 0.6858 (tt0) REVERT: f 128 MET cc_start: 0.6979 (mmt) cc_final: 0.6280 (ptt) outliers start: 28 outliers final: 22 residues processed: 109 average time/residue: 0.0751 time to fit residues: 10.4241 Evaluate side-chains 109 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 64 PHE Chi-restraints excluded: chain g residue 87 CYS Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain n residue 267 LEU Chi-restraints excluded: chain n residue 281 THR Chi-restraints excluded: chain n residue 282 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.0570 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.217554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.179762 restraints weight = 5779.177| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.29 r_work: 0.3802 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4947 Z= 0.113 Angle : 0.514 5.846 6710 Z= 0.272 Chirality : 0.038 0.145 781 Planarity : 0.004 0.045 808 Dihedral : 7.240 58.921 832 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.08 % Allowed : 18.46 % Favored : 76.46 % 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: 0.77 (0.36), residues: 581 helix: 3.84 (0.31), residues: 226 sheet: -0.39 (0.64), residues: 71 loop : -2.26 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 117 TYR 0.008 0.001 TYR n 266 PHE 0.007 0.001 PHE f 87 TRP 0.012 0.001 TRP f 59 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4939) covalent geometry : angle 0.51322 ( 6694) SS BOND : bond 0.00300 ( 8) SS BOND : angle 0.81492 ( 16) hydrogen bonds : bond 0.04077 ( 247) hydrogen bonds : angle 3.74636 ( 714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: e 91 GLU cc_start: 0.7417 (tp30) cc_final: 0.6868 (tt0) REVERT: f 128 MET cc_start: 0.6997 (mmt) cc_final: 0.6202 (ptt) outliers start: 27 outliers final: 22 residues processed: 106 average time/residue: 0.0654 time to fit residues: 9.0532 Evaluate side-chains 110 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 64 PHE Chi-restraints excluded: chain g residue 87 CYS Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain n residue 267 LEU Chi-restraints excluded: chain n residue 281 THR Chi-restraints excluded: chain n residue 282 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.220346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.189577 restraints weight = 5618.722| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.90 r_work: 0.3878 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4947 Z= 0.118 Angle : 0.516 5.633 6710 Z= 0.275 Chirality : 0.039 0.156 781 Planarity : 0.004 0.045 808 Dihedral : 7.104 57.743 830 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.52 % Allowed : 19.77 % Favored : 75.71 % 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: 0.75 (0.36), residues: 581 helix: 3.83 (0.31), residues: 226 sheet: -0.61 (0.69), residues: 61 loop : -2.17 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 117 TYR 0.011 0.001 TYR e 36 PHE 0.008 0.001 PHE f 87 TRP 0.014 0.001 TRP f 59 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4939) covalent geometry : angle 0.51508 ( 6694) SS BOND : bond 0.00331 ( 8) SS BOND : angle 0.92732 ( 16) hydrogen bonds : bond 0.04184 ( 247) hydrogen bonds : angle 3.76210 ( 714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.174 Fit side-chains REVERT: b 35 LEU cc_start: 0.7602 (tt) cc_final: 0.6590 (tp) REVERT: e 91 GLU cc_start: 0.7230 (tp30) cc_final: 0.6842 (tt0) outliers start: 24 outliers final: 21 residues processed: 102 average time/residue: 0.0751 time to fit residues: 9.8163 Evaluate side-chains 107 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 64 PHE Chi-restraints excluded: chain g residue 87 CYS Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain n residue 267 LEU Chi-restraints excluded: chain n residue 281 THR Chi-restraints excluded: chain n residue 282 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.217899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.186628 restraints weight = 5677.279| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.94 r_work: 0.3768 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4947 Z= 0.141 Angle : 0.567 6.448 6710 Z= 0.299 Chirality : 0.040 0.165 781 Planarity : 0.004 0.044 808 Dihedral : 7.310 54.975 830 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.52 % Allowed : 20.72 % Favored : 74.76 % 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: 0.65 (0.36), residues: 581 helix: 3.68 (0.31), residues: 226 sheet: -0.61 (0.60), residues: 82 loop : -2.27 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 117 TYR 0.013 0.001 TYR e 36 PHE 0.010 0.001 PHE g 118 TRP 0.017 0.002 TRP f 59 HIS 0.004 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4939) covalent geometry : angle 0.55810 ( 6694) SS BOND : bond 0.00388 ( 8) SS BOND : angle 2.10648 ( 16) hydrogen bonds : bond 0.04768 ( 247) hydrogen bonds : angle 3.94007 ( 714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.190 Fit side-chains REVERT: e 91 GLU cc_start: 0.7273 (tp30) cc_final: 0.6825 (tt0) REVERT: e 110 PHE cc_start: 0.6595 (m-80) cc_final: 0.5625 (p90) outliers start: 24 outliers final: 24 residues processed: 101 average time/residue: 0.0658 time to fit residues: 8.7854 Evaluate side-chains 109 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 97 VAL Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 39 SER Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 64 PHE Chi-restraints excluded: chain g residue 87 CYS Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain m residue 254 VAL Chi-restraints excluded: chain n residue 267 LEU Chi-restraints excluded: chain n residue 281 THR Chi-restraints excluded: chain n residue 282 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.218167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186828 restraints weight = 5751.218| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.95 r_work: 0.3787 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4947 Z= 0.138 Angle : 0.565 6.065 6710 Z= 0.298 Chirality : 0.040 0.154 781 Planarity : 0.004 0.044 808 Dihedral : 7.253 51.264 830 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.71 % Allowed : 20.90 % Favored : 74.39 % 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: 0.65 (0.36), residues: 581 helix: 3.67 (0.31), residues: 226 sheet: -0.59 (0.60), residues: 82 loop : -2.26 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 117 TYR 0.014 0.001 TYR e 36 PHE 0.010 0.001 PHE f 87 TRP 0.018 0.001 TRP f 59 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4939) covalent geometry : angle 0.55685 ( 6694) SS BOND : bond 0.00398 ( 8) SS BOND : angle 2.04405 ( 16) hydrogen bonds : bond 0.04696 ( 247) hydrogen bonds : angle 3.94024 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1319.44 seconds wall clock time: 23 minutes 45.24 seconds (1425.24 seconds total)